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Agilent technologies bioanalyzer
Representative <t>bioanalyzer</t> images of cfDNA libraries. (A) Human and (B) mouse samples.
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Images

1) Product Images from "Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model"

Article Title: Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model

Journal: Frontiers in Genetics

doi: 10.3389/fgene.2018.00006

Representative bioanalyzer images of cfDNA libraries. (A) Human and (B) mouse samples.
Figure Legend Snippet: Representative bioanalyzer images of cfDNA libraries. (A) Human and (B) mouse samples.

Techniques Used:

Representative bioanalyzer images of freshly isolated and bead-purified cfDNA. (A–C) Healthy human control, (D–F) WT mouse, and (G–I) PDAC mouse. The left columns depict the freshly isolated starting cfDNA (green arrow and dotted line) and the contaminating high molecular weight DNA (black arrow) evident by a wide peak. The middle column depicts the high molecular weight DNA removed from the same samples shown in (A–G) by the SPRI AMPure bead purification step after the 0.5X dilution step. The right column shows the purified cfDNA as recovered form the SPRI AMPure bead purification step after the 1.6X dilution step from the same samples shown in (A–G) . The desired cfDNA peak is visible ∼150–200 bp (green arrow and dotted line).
Figure Legend Snippet: Representative bioanalyzer images of freshly isolated and bead-purified cfDNA. (A–C) Healthy human control, (D–F) WT mouse, and (G–I) PDAC mouse. The left columns depict the freshly isolated starting cfDNA (green arrow and dotted line) and the contaminating high molecular weight DNA (black arrow) evident by a wide peak. The middle column depicts the high molecular weight DNA removed from the same samples shown in (A–G) by the SPRI AMPure bead purification step after the 0.5X dilution step. The right column shows the purified cfDNA as recovered form the SPRI AMPure bead purification step after the 1.6X dilution step from the same samples shown in (A–G) . The desired cfDNA peak is visible ∼150–200 bp (green arrow and dotted line).

Techniques Used: Isolation, Purification, Molecular Weight

Representative bioanalyzer profiles of cfDNA. (A) The concentration of cfDNA per ml of plasma (human control and lung cancer and mice) or serum (human PNET) is shown for each of the samples analyzed. The horizontal bar indicates the average values for each sample set. (B) Healthy human control #6, (C) PNET patient #4, (D) lung cancer patient #9, (E) WT mouse #1, and (F) PDAC mouse #3. A peak with the highest DNA amount was detected around 160 bp (green arrow and dotted line). Secondary peaks at ∼320 bp (blue arrow and dotted line) were visible in all samples except the WT mouse control. Contaminating high molecular weight DNA was present in some samples (black arrow in B ).
Figure Legend Snippet: Representative bioanalyzer profiles of cfDNA. (A) The concentration of cfDNA per ml of plasma (human control and lung cancer and mice) or serum (human PNET) is shown for each of the samples analyzed. The horizontal bar indicates the average values for each sample set. (B) Healthy human control #6, (C) PNET patient #4, (D) lung cancer patient #9, (E) WT mouse #1, and (F) PDAC mouse #3. A peak with the highest DNA amount was detected around 160 bp (green arrow and dotted line). Secondary peaks at ∼320 bp (blue arrow and dotted line) were visible in all samples except the WT mouse control. Contaminating high molecular weight DNA was present in some samples (black arrow in B ).

Techniques Used: Concentration Assay, Mouse Assay, Molecular Weight

2) Product Images from "Bead-linked transposomes enable a normalization-free workflow for NGS library preparation"

Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation

Journal: BMC Genomics

doi: 10.1186/s12864-018-5096-9

Application of Nextera DNA Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum
Figure Legend Snippet: Application of Nextera DNA Flex to bacterial amplicons. a Libraries prepared using Nextera DNA Flex showed more consistent, even coverage compared with libraries prepared using Nextera XT; data depicts the sequence coverage of libraries prepared from the 3 kb E. coli amplicon. b PCR products ranging in size from 50 bp to 3 kb amplified from E. coli gDNA visualized on a 1% agarose gel. c Libraries prepared from a 1 ng input of these E. coli amplicons resulted in Bioanalyzer traces that depicted a slight increase in fragment size with increasing amplicon size. d Libraries were sequenced on a MiSeq and coverage of the E. coli genome determined for the different amplicon fragment size inputs. Sequenceable libraries were generated from amplicons ranging in size from 50 bp to 3 kb. e When sequencing data was downsampled to 25,000 reads, the larger fragment inputs were reaching a coverage maximum

Techniques Used: Sequencing, Amplification, Polymerase Chain Reaction, Agarose Gel Electrophoresis, Generated

Bioanalyzer traces of libraries prepared from various sample types and species. a Libraries prepared from samples with a varied degree of formalin fixation; a higher ΔCq indicates more FFPE-induced DNA degradation compared with a positive control. b Increasing FFPE-induced DNA degradation has a small effect on average fragment size but a marked effect on the total library yield. Increasing the DNA input from 100 ng to 150 ng did not increase library yield, indicating bead saturation at a DNA input of around 100 ng regardless of the degree of DNA degradation. c Libraries prepared from gDNA from a range of animal (human, Angus, and mouse), plant (Arabidopsis and alfalfa), and bacterial ( E. coli and B. cereus ) species
Figure Legend Snippet: Bioanalyzer traces of libraries prepared from various sample types and species. a Libraries prepared from samples with a varied degree of formalin fixation; a higher ΔCq indicates more FFPE-induced DNA degradation compared with a positive control. b Increasing FFPE-induced DNA degradation has a small effect on average fragment size but a marked effect on the total library yield. Increasing the DNA input from 100 ng to 150 ng did not increase library yield, indicating bead saturation at a DNA input of around 100 ng regardless of the degree of DNA degradation. c Libraries prepared from gDNA from a range of animal (human, Angus, and mouse), plant (Arabidopsis and alfalfa), and bacterial ( E. coli and B. cereus ) species

Techniques Used: Formalin-fixed Paraffin-Embedded, Positive Control

Application of Nextera DNA Flex to human amplicons. a Human leukocyte antigen (HLA) gene amplicons used as inputs for library preparation visualized on a 1% agarose gel. Lanes and expected amplicon sizes are as follows: 1, KBL Ladder; 2, HLA-A (4.1 kb); 3, HLA-B (2.8 kb); 4, HLA-C (4.2 kb); 5, HLA-DPA1 (10.3 kb); 6, HLA-DPB1 (9.7 kb); 7, HLA-DQA1 (7.3 kb); 8, HLA-DRB2 (4.6 kb); 9, HLA-DQB1 (7.1 kb). b Nextera DNA Flex library yields of all HLA amplicons were within the acceptable values of > 4 ng/μl and 9–13 ng/μl for 1 ng and 100–300 ng inputs, respectively. The yields for Nextera DNA Flex libraries were higher than for those prepared using TruSight HLA; for TruSight HLA, libraries were prepared from 1 ng of each amplicon and then pooled. c The Bioanalyzer profiles depict library fragment size distributions within the acceptable range; the distribution is narrower for the Nextera DNA Flex libraries (1 ng DNA inputs) than the TruSight HLA libraries. d Sequencing coverage depth and uniformity were higher for libraries prepared using Nextera DNA Flex (Flex) compared with TruSight HLA (TS HLA). e Libraries were sequenced on a NextSeq 550, with downsampling to 25,000 reads per amplicon. Library preparation using Nextera DNA Flex (orange) resulted in more uniform coverage of the entire human mitochondrial chromosome when compared with Nextera XT (grey). The location of the PCR primers used to create the two mtDNA amplicons are depicted by blue and red arrows. Dotted-line rectangle indicates the D-Loop region. f Zoomed in view shows more uniform coverage with Nextera DNA Flex within the D-Loop region
Figure Legend Snippet: Application of Nextera DNA Flex to human amplicons. a Human leukocyte antigen (HLA) gene amplicons used as inputs for library preparation visualized on a 1% agarose gel. Lanes and expected amplicon sizes are as follows: 1, KBL Ladder; 2, HLA-A (4.1 kb); 3, HLA-B (2.8 kb); 4, HLA-C (4.2 kb); 5, HLA-DPA1 (10.3 kb); 6, HLA-DPB1 (9.7 kb); 7, HLA-DQA1 (7.3 kb); 8, HLA-DRB2 (4.6 kb); 9, HLA-DQB1 (7.1 kb). b Nextera DNA Flex library yields of all HLA amplicons were within the acceptable values of > 4 ng/μl and 9–13 ng/μl for 1 ng and 100–300 ng inputs, respectively. The yields for Nextera DNA Flex libraries were higher than for those prepared using TruSight HLA; for TruSight HLA, libraries were prepared from 1 ng of each amplicon and then pooled. c The Bioanalyzer profiles depict library fragment size distributions within the acceptable range; the distribution is narrower for the Nextera DNA Flex libraries (1 ng DNA inputs) than the TruSight HLA libraries. d Sequencing coverage depth and uniformity were higher for libraries prepared using Nextera DNA Flex (Flex) compared with TruSight HLA (TS HLA). e Libraries were sequenced on a NextSeq 550, with downsampling to 25,000 reads per amplicon. Library preparation using Nextera DNA Flex (orange) resulted in more uniform coverage of the entire human mitochondrial chromosome when compared with Nextera XT (grey). The location of the PCR primers used to create the two mtDNA amplicons are depicted by blue and red arrows. Dotted-line rectangle indicates the D-Loop region. f Zoomed in view shows more uniform coverage with Nextera DNA Flex within the D-Loop region

Techniques Used: Agarose Gel Electrophoresis, Amplification, Sequencing, Polymerase Chain Reaction

3) Product Images from "Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model"

Article Title: Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model

Journal: Frontiers in Genetics

doi: 10.3389/fgene.2018.00006

Representative bioanalyzer images of cfDNA libraries. (A) Human and (B) mouse samples.
Figure Legend Snippet: Representative bioanalyzer images of cfDNA libraries. (A) Human and (B) mouse samples.

Techniques Used:

Representative bioanalyzer profiles of cfDNA. (A) The concentration of cfDNA per ml of plasma (human control and lung cancer and mice) or serum (human PNET) is shown for each of the samples analyzed. The horizontal bar indicates the average values for each sample set. (B) Healthy human control #6, (C) PNET patient #4, (D) lung cancer patient #9, (E) WT mouse #1, and (F) PDAC mouse #3. A peak with the highest DNA amount was detected around 160 bp (green arrow and dotted line). Secondary peaks at ∼320 bp (blue arrow and dotted line) were visible in all samples except the WT mouse control. Contaminating high molecular weight DNA was present in some samples (black arrow in B ).
Figure Legend Snippet: Representative bioanalyzer profiles of cfDNA. (A) The concentration of cfDNA per ml of plasma (human control and lung cancer and mice) or serum (human PNET) is shown for each of the samples analyzed. The horizontal bar indicates the average values for each sample set. (B) Healthy human control #6, (C) PNET patient #4, (D) lung cancer patient #9, (E) WT mouse #1, and (F) PDAC mouse #3. A peak with the highest DNA amount was detected around 160 bp (green arrow and dotted line). Secondary peaks at ∼320 bp (blue arrow and dotted line) were visible in all samples except the WT mouse control. Contaminating high molecular weight DNA was present in some samples (black arrow in B ).

Techniques Used: Concentration Assay, Mouse Assay, Molecular Weight

4) Product Images from "Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination"

Article Title: Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination

Journal: Journal of Extracellular Vesicles

doi: 10.3402/jev.v5.30281

Pico 6000 RNA Chip electropherograms run in Agilent 2100 Bioanalyzer for RNA samples coming from UEVs extracted with different methods: (a) FastRNA; (b) Qiagen; (c) TRIzol; (d) Norgen; (e) Nucleo-Spin; (f) Quick RNA; (g) mirVana; nt – nucleotide size, grey arrow – marker peak, FU – fluorescence units.
Figure Legend Snippet: Pico 6000 RNA Chip electropherograms run in Agilent 2100 Bioanalyzer for RNA samples coming from UEVs extracted with different methods: (a) FastRNA; (b) Qiagen; (c) TRIzol; (d) Norgen; (e) Nucleo-Spin; (f) Quick RNA; (g) mirVana; nt – nucleotide size, grey arrow – marker peak, FU – fluorescence units.

Techniques Used: Chromatin Immunoprecipitation, Marker, Fluorescence

Profiles of isolated RNA analyzed by Agilent 2100 Bioanalyzer in PicoChip (electropherograms). (a) UEVs RNA enriched via HFD and isolated with Norgen Kit; (b) cellular RNA extracted with FastRNA Kit; (c) UEVs with spike-in of cellular RNA; (d) cellular RNA re-extracted with Norgen Kit; (e) UEVs RNA, cellular RNA and UEVs+cellular RNA electropherograms merged together according to nucleotide size axis; (f) bacterial RNA; (g) cellular RNA and bacterial RNA mixed and run together; (h) cellular RNA and bacterial RNA electropherograms merged together according to nucleotide size axis. Grey arrow – marker dye; blue arrow – UEVs rRNA; red arrow – 18s and 28s rRNA; black arrow – 16s and 23s rRNA.
Figure Legend Snippet: Profiles of isolated RNA analyzed by Agilent 2100 Bioanalyzer in PicoChip (electropherograms). (a) UEVs RNA enriched via HFD and isolated with Norgen Kit; (b) cellular RNA extracted with FastRNA Kit; (c) UEVs with spike-in of cellular RNA; (d) cellular RNA re-extracted with Norgen Kit; (e) UEVs RNA, cellular RNA and UEVs+cellular RNA electropherograms merged together according to nucleotide size axis; (f) bacterial RNA; (g) cellular RNA and bacterial RNA mixed and run together; (h) cellular RNA and bacterial RNA electropherograms merged together according to nucleotide size axis. Grey arrow – marker dye; blue arrow – UEVs rRNA; red arrow – 18s and 28s rRNA; black arrow – 16s and 23s rRNA.

Techniques Used: Isolation, Marker

Small RNA Chip electropherograms run in Agilent 2100 Bioanalyzer for RNA samples coming from UEVs extracted with different methods: (a) FastRNA; (b) Qiagen; (c) TRIzol; (d) Norgen; (e) Nucleo-Spin; (f) Quick RNA; (g) mirVana; nt – nucleotide size, grey arrow – marker peak, FU – fluorescence units.
Figure Legend Snippet: Small RNA Chip electropherograms run in Agilent 2100 Bioanalyzer for RNA samples coming from UEVs extracted with different methods: (a) FastRNA; (b) Qiagen; (c) TRIzol; (d) Norgen; (e) Nucleo-Spin; (f) Quick RNA; (g) mirVana; nt – nucleotide size, grey arrow – marker peak, FU – fluorescence units.

Techniques Used: Chromatin Immunoprecipitation, Marker, Fluorescence

5) Product Images from "Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)"

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkm510

Size distribution of mRNA, cRNA and dsDNA on Agilent 2100 Bioanalyzer 6000 Nanochips. ( a ) Universal Human Reference (UHR) RNA and sense-RNA template library after IVT-amplification. Lane L displays the ladder (25, 200, 500, 1000, 2000 and 4000 nt). Lane 1 contains fresh UHR RNA. Lanes 2, 3 and 4 display three individual IVT-amplifications of sense-RNA using total RNA displayed in lane 1. ( b ) Size distribution of fresh, frozen, FFPE-RNA and amplified cRNA. Lane L displays the same ladder as observed in (a). Lane 1 contains fresh human breast RNA. Lane 2 contains total RNA from the 10-year-old frozen human breast cancer tissue. Lane 3 contains total RNA from the matched 10-year-old FFPE human breast cancer tissue. Lane 4 contains cRNA obtained by IVT-amplifications of 10-year-old frozen RNA (lane 2). Lanes 5 contains cRNA obtained by direct IVT-amplification of the 10-year-old FFPE-RNA (lane 3). Lanes 6 contains amplified cRNA obtained by CT-RT and IVT-amplification of the same 10-year-old FFPE-RNA. ( c ) Size distribution of double-stranded DNA on a Bioanalyzer 2100 Agilent nanochip. Lane L displays the ladder. Lane 1 displays dsDNA obtained from 10-year-old frozen RNA. Lane 2 displays dsDNA obtained from 10-year-old FFPE-RNA. Lane 3 shows dsDNA obtained after CT-RT and double-strand DNA synthesis of the same 10-year-old FFPE-RNA. (See Supplementary Data for fragmented RNA profiles)
Figure Legend Snippet: Size distribution of mRNA, cRNA and dsDNA on Agilent 2100 Bioanalyzer 6000 Nanochips. ( a ) Universal Human Reference (UHR) RNA and sense-RNA template library after IVT-amplification. Lane L displays the ladder (25, 200, 500, 1000, 2000 and 4000 nt). Lane 1 contains fresh UHR RNA. Lanes 2, 3 and 4 display three individual IVT-amplifications of sense-RNA using total RNA displayed in lane 1. ( b ) Size distribution of fresh, frozen, FFPE-RNA and amplified cRNA. Lane L displays the same ladder as observed in (a). Lane 1 contains fresh human breast RNA. Lane 2 contains total RNA from the 10-year-old frozen human breast cancer tissue. Lane 3 contains total RNA from the matched 10-year-old FFPE human breast cancer tissue. Lane 4 contains cRNA obtained by IVT-amplifications of 10-year-old frozen RNA (lane 2). Lanes 5 contains cRNA obtained by direct IVT-amplification of the 10-year-old FFPE-RNA (lane 3). Lanes 6 contains amplified cRNA obtained by CT-RT and IVT-amplification of the same 10-year-old FFPE-RNA. ( c ) Size distribution of double-stranded DNA on a Bioanalyzer 2100 Agilent nanochip. Lane L displays the ladder. Lane 1 displays dsDNA obtained from 10-year-old frozen RNA. Lane 2 displays dsDNA obtained from 10-year-old FFPE-RNA. Lane 3 shows dsDNA obtained after CT-RT and double-strand DNA synthesis of the same 10-year-old FFPE-RNA. (See Supplementary Data for fragmented RNA profiles)

Techniques Used: Amplification, Formalin-fixed Paraffin-Embedded, DNA Synthesis

Electropherogram of total RNA recovered from FFPE samples utilized in CT-RT experiments. Total RNA extracted from 10-year-old breast cancer and 3-year-old cervical FFPE tissues were loaded on a Agilent 2100 Bioanalyzer 6000 Nanochip. Electropherograms were obtained with the 2100 expert software from Agilent, version B.02.03.SI307. 18S and 28S ribosomal RNA peaks are not detected in either FFPE sample, indicative of severe degradation.
Figure Legend Snippet: Electropherogram of total RNA recovered from FFPE samples utilized in CT-RT experiments. Total RNA extracted from 10-year-old breast cancer and 3-year-old cervical FFPE tissues were loaded on a Agilent 2100 Bioanalyzer 6000 Nanochip. Electropherograms were obtained with the 2100 expert software from Agilent, version B.02.03.SI307. 18S and 28S ribosomal RNA peaks are not detected in either FFPE sample, indicative of severe degradation.

Techniques Used: Formalin-fixed Paraffin-Embedded, Software

6) Product Images from "Comparison of DNA Quantification Methods for Next Generation Sequencing"

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing

Journal: Scientific Reports

doi: 10.1038/srep24067

Comparison of four titration techniques for NGS. ( a ) Diagram of the Next generation sequencing (NGS) experimental design. Using four quantification methods, we titrated DNA libraries prepared from HeLa cells, following manufacturers’ instructions. Six different indexes were added at the amplification step. Of the eight lanes on the NGS flowcell, four lanes were used to compare each method (unique index lane) and four lanes for pooling accuracy (pool of six indexes per lane). ( b ) Bioanalyzer image of the libraries, showing a homogenous smear of DNA from 280 to 450 bp. All six indexes show similarly average sizes. ( c ) Result of the quantification for all indexes using QuBit, qPCR, ddPCR and ddPCR-Tail approaches, respectively. All quantifications (except ddPCR-Tail) were done following manufacturer instructions (Invitrogen, BioRad, and KapaBiosystem). The ddPCR-Tail strategy used the same apparatus as the ddPCR with slight modifications (50 nM primers; three-step PCR-annealing at 65 °C for 30 seconds, extension time of 30 seconds at 72 °C). Experiments done in triplicate, mean calculated using dilution curve (average of 12 values per quantification, 6 for QuBit). Mean ± SD shown.
Figure Legend Snippet: Comparison of four titration techniques for NGS. ( a ) Diagram of the Next generation sequencing (NGS) experimental design. Using four quantification methods, we titrated DNA libraries prepared from HeLa cells, following manufacturers’ instructions. Six different indexes were added at the amplification step. Of the eight lanes on the NGS flowcell, four lanes were used to compare each method (unique index lane) and four lanes for pooling accuracy (pool of six indexes per lane). ( b ) Bioanalyzer image of the libraries, showing a homogenous smear of DNA from 280 to 450 bp. All six indexes show similarly average sizes. ( c ) Result of the quantification for all indexes using QuBit, qPCR, ddPCR and ddPCR-Tail approaches, respectively. All quantifications (except ddPCR-Tail) were done following manufacturer instructions (Invitrogen, BioRad, and KapaBiosystem). The ddPCR-Tail strategy used the same apparatus as the ddPCR with slight modifications (50 nM primers; three-step PCR-annealing at 65 °C for 30 seconds, extension time of 30 seconds at 72 °C). Experiments done in triplicate, mean calculated using dilution curve (average of 12 values per quantification, 6 for QuBit). Mean ± SD shown.

Techniques Used: Titration, Next-Generation Sequencing, Amplification, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction

Titration of six NGS libraries with low abundance with qPCR and ddPCR Tail. ( a ) Comparison of two methods for low abundance NGS libraries, titration results using qPCR and the ddPCR-Tail system. Assay done in triplicate and mean calculated using dilution correction factors (average of 18 values per sample). Mean ± SD shown. ( b ) Bioanalyzer image results used to calculate final molarity for the qPCR measurement, algorithm provided by KapaBiosystem using the average size of the NGS library combined with the qPCR standard curve. ( c ) All libraries were successfully quantified with high confidence (linear regression all in 0.9), ddPCR Tail strategy showed a better overall linearity regardless of the heterogeneity of the libraries.
Figure Legend Snippet: Titration of six NGS libraries with low abundance with qPCR and ddPCR Tail. ( a ) Comparison of two methods for low abundance NGS libraries, titration results using qPCR and the ddPCR-Tail system. Assay done in triplicate and mean calculated using dilution correction factors (average of 18 values per sample). Mean ± SD shown. ( b ) Bioanalyzer image results used to calculate final molarity for the qPCR measurement, algorithm provided by KapaBiosystem using the average size of the NGS library combined with the qPCR standard curve. ( c ) All libraries were successfully quantified with high confidence (linear regression all in 0.9), ddPCR Tail strategy showed a better overall linearity regardless of the heterogeneity of the libraries.

Techniques Used: Titration, Next-Generation Sequencing, Real-time Polymerase Chain Reaction

7) Product Images from "RNA sequencing data of Notch ligand treated human dental pulp cells"

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells

Journal: Data in Brief

doi: 10.1016/j.dib.2018.01.058

Library quality and size check using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.
Figure Legend Snippet: Library quality and size check using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.

Techniques Used:

Quality check of input total RNA using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.
Figure Legend Snippet: Quality check of input total RNA using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.

Techniques Used:

8) Product Images from "RNA sequencing data of Notch ligand treated human dental pulp cells"

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells

Journal: Data in Brief

doi: 10.1016/j.dib.2018.01.058

Library quality and size check using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.
Figure Legend Snippet: Library quality and size check using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.

Techniques Used:

Quality check of input total RNA using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.
Figure Legend Snippet: Quality check of input total RNA using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.

Techniques Used:

9) Product Images from "Comparison of DNA Quantification Methods for Next Generation Sequencing"

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing

Journal: Scientific Reports

doi: 10.1038/srep24067

Comparison of four titration techniques for NGS. ( a ) Diagram of the Next generation sequencing (NGS) experimental design. Using four quantification methods, we titrated DNA libraries prepared from HeLa cells, following manufacturers’ instructions. Six different indexes were added at the amplification step. Of the eight lanes on the NGS flowcell, four lanes were used to compare each method (unique index lane) and four lanes for pooling accuracy (pool of six indexes per lane). ( b ) Bioanalyzer image of the libraries, showing a homogenous smear of DNA from 280 to 450 bp. All six indexes show similarly average sizes. ( c ) Result of the quantification for all indexes using QuBit, qPCR, ddPCR and ddPCR-Tail approaches, respectively. All quantifications (except ddPCR-Tail) were done following manufacturer instructions (Invitrogen, BioRad, and KapaBiosystem). The ddPCR-Tail strategy used the same apparatus as the ddPCR with slight modifications (50 nM primers; three-step PCR-annealing at 65 °C for 30 seconds, extension time of 30 seconds at 72 °C). Experiments done in triplicate, mean calculated using dilution curve (average of 12 values per quantification, 6 for QuBit). Mean ± SD shown.
Figure Legend Snippet: Comparison of four titration techniques for NGS. ( a ) Diagram of the Next generation sequencing (NGS) experimental design. Using four quantification methods, we titrated DNA libraries prepared from HeLa cells, following manufacturers’ instructions. Six different indexes were added at the amplification step. Of the eight lanes on the NGS flowcell, four lanes were used to compare each method (unique index lane) and four lanes for pooling accuracy (pool of six indexes per lane). ( b ) Bioanalyzer image of the libraries, showing a homogenous smear of DNA from 280 to 450 bp. All six indexes show similarly average sizes. ( c ) Result of the quantification for all indexes using QuBit, qPCR, ddPCR and ddPCR-Tail approaches, respectively. All quantifications (except ddPCR-Tail) were done following manufacturer instructions (Invitrogen, BioRad, and KapaBiosystem). The ddPCR-Tail strategy used the same apparatus as the ddPCR with slight modifications (50 nM primers; three-step PCR-annealing at 65 °C for 30 seconds, extension time of 30 seconds at 72 °C). Experiments done in triplicate, mean calculated using dilution curve (average of 12 values per quantification, 6 for QuBit). Mean ± SD shown.

Techniques Used: Titration, Next-Generation Sequencing, Amplification, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction

Titration of six NGS libraries with low abundance with qPCR and ddPCR Tail. ( a ) Comparison of two methods for low abundance NGS libraries, titration results using qPCR and the ddPCR-Tail system. Assay done in triplicate and mean calculated using dilution correction factors (average of 18 values per sample). Mean ± SD shown. ( b ) Bioanalyzer image results used to calculate final molarity for the qPCR measurement, algorithm provided by KapaBiosystem using the average size of the NGS library combined with the qPCR standard curve. ( c ) All libraries were successfully quantified with high confidence (linear regression all in 0.9), ddPCR Tail strategy showed a better overall linearity regardless of the heterogeneity of the libraries.
Figure Legend Snippet: Titration of six NGS libraries with low abundance with qPCR and ddPCR Tail. ( a ) Comparison of two methods for low abundance NGS libraries, titration results using qPCR and the ddPCR-Tail system. Assay done in triplicate and mean calculated using dilution correction factors (average of 18 values per sample). Mean ± SD shown. ( b ) Bioanalyzer image results used to calculate final molarity for the qPCR measurement, algorithm provided by KapaBiosystem using the average size of the NGS library combined with the qPCR standard curve. ( c ) All libraries were successfully quantified with high confidence (linear regression all in 0.9), ddPCR Tail strategy showed a better overall linearity regardless of the heterogeneity of the libraries.

Techniques Used: Titration, Next-Generation Sequencing, Real-time Polymerase Chain Reaction

10) Product Images from "An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries"

Article Title: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries

Journal: Scientific Reports

doi: 10.1038/srep37137

Quantitative evaluation of libraries prepared from oral gingival tissue. The quality of the libraries generated from gingival tissue was assessed after in vitro transcription and again after final cDNA synthesis. ( a ) Bioanalyzer (Agilent) trace showing the fragment size distributions for the six libraries after amplification by in vitro transcription. The traces from the automated protocol are shown in red while the traces from the manual protocol are shown in blue. The traces were also used to estimate the concentrations of the samples, which are illustrated in the left part of the boxplot ( c ). After the final cDNA synthesis the libraries were evaluated by quantitative PCR (qPCR) ( b ). The black vertical line marks the signal threshold at which point the cycle threshold (Ct) values were noted. The Ct values for the libraries as obtained from the qPCR are plotted in the right part of the boxplot ( c ).
Figure Legend Snippet: Quantitative evaluation of libraries prepared from oral gingival tissue. The quality of the libraries generated from gingival tissue was assessed after in vitro transcription and again after final cDNA synthesis. ( a ) Bioanalyzer (Agilent) trace showing the fragment size distributions for the six libraries after amplification by in vitro transcription. The traces from the automated protocol are shown in red while the traces from the manual protocol are shown in blue. The traces were also used to estimate the concentrations of the samples, which are illustrated in the left part of the boxplot ( c ). After the final cDNA synthesis the libraries were evaluated by quantitative PCR (qPCR) ( b ). The black vertical line marks the signal threshold at which point the cycle threshold (Ct) values were noted. The Ct values for the libraries as obtained from the qPCR are plotted in the right part of the boxplot ( c ).

Techniques Used: Generated, In Vitro, Amplification, Real-time Polymerase Chain Reaction

Quantitative evaluation of libraries prepared from total reference RNA. Sample-to-sample variation was investigated by small red triangles assessing the libraries at two points during the library preparation process. ( a ) The first evaluation is performed after in vitro transcription and checks the library concentrations and fragment lengths using a Bioanalyzer (Agilent). ( b ) After reverse transcription, a quantitative PCR (qPCR) was carried out to determine the suitable number of PCR cycles when indexing the finished libraries. The black vertical line marks the signal threshold at which point the cycle threshold (Ct) values were obtained. The spread of Ct values is illustrated in the boxplot ( c ), which also shows the variation in sample concentration as measured by the Bioanalyzer after in vitro transcription.
Figure Legend Snippet: Quantitative evaluation of libraries prepared from total reference RNA. Sample-to-sample variation was investigated by small red triangles assessing the libraries at two points during the library preparation process. ( a ) The first evaluation is performed after in vitro transcription and checks the library concentrations and fragment lengths using a Bioanalyzer (Agilent). ( b ) After reverse transcription, a quantitative PCR (qPCR) was carried out to determine the suitable number of PCR cycles when indexing the finished libraries. The black vertical line marks the signal threshold at which point the cycle threshold (Ct) values were obtained. The spread of Ct values is illustrated in the boxplot ( c ), which also shows the variation in sample concentration as measured by the Bioanalyzer after in vitro transcription.

Techniques Used: In Vitro, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Concentration Assay

11) Product Images from "Venom On-a-Chip: A Fast and Efficient Method for Comparative Venomics"

Article Title: Venom On-a-Chip: A Fast and Efficient Method for Comparative Venomics

Journal: Toxins

doi: 10.3390/toxins9060179

Comparison of reverse-phase HPLC venom fractions ( top panel ) separated by traditional SDS-PAGE ( middle ) and the on-chip Bioanalyzer ( bottom ) using C. scutulatus venom type A ( left ) and B ( right ). Only those fractions with the most relevant differences between the two venoms are shown. Molecular mass markers are at the left side of each gels. Proteomic-guided assignment of the chromatographic fractions to toxin families and relative molecular weights are shown in Table 2 .
Figure Legend Snippet: Comparison of reverse-phase HPLC venom fractions ( top panel ) separated by traditional SDS-PAGE ( middle ) and the on-chip Bioanalyzer ( bottom ) using C. scutulatus venom type A ( left ) and B ( right ). Only those fractions with the most relevant differences between the two venoms are shown. Molecular mass markers are at the left side of each gels. Proteomic-guided assignment of the chromatographic fractions to toxin families and relative molecular weights are shown in Table 2 .

Techniques Used: High Performance Liquid Chromatography, SDS Page, Chromatin Immunoprecipitation

( A ) Flowchart summarizing the steps involved in protein analysis of crude venom samples by means of on-chip electrophoresis, RP-HPLC and SDS-PAGE; ( B ) Example of two overlapped electropherograms ( left ) and the corresponding digital gel ( right ) from on-chip electrophoresis on the Agilent Bioanalyzer. Each sample is loaded with two internal standards: a “lower” (1.6 kDa) and “upper” (95 kDa) markers are used to align the electropherograms. The migration time of each peak is used to create the marker “bin” (in grey). All peaks falling in the bin are scored as present (1). Here we used venoms from Crotalus scutulatus type A (blue) and B (red) (refer to ‘Intraspecific variation’ for details); the latter has two distinctive peaks at approximately 23 kDa (*) and 67 kDa (**) likely corresponding to PI-SVMPs and PIII-SVMPs.
Figure Legend Snippet: ( A ) Flowchart summarizing the steps involved in protein analysis of crude venom samples by means of on-chip electrophoresis, RP-HPLC and SDS-PAGE; ( B ) Example of two overlapped electropherograms ( left ) and the corresponding digital gel ( right ) from on-chip electrophoresis on the Agilent Bioanalyzer. Each sample is loaded with two internal standards: a “lower” (1.6 kDa) and “upper” (95 kDa) markers are used to align the electropherograms. The migration time of each peak is used to create the marker “bin” (in grey). All peaks falling in the bin are scored as present (1). Here we used venoms from Crotalus scutulatus type A (blue) and B (red) (refer to ‘Intraspecific variation’ for details); the latter has two distinctive peaks at approximately 23 kDa (*) and 67 kDa (**) likely corresponding to PI-SVMPs and PIII-SVMPs.

Techniques Used: Chromatin Immunoprecipitation, Electrophoresis, High Performance Liquid Chromatography, SDS Page, Migration, Marker

12) Product Images from "Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes"

Article Title: Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

Journal: PLoS ONE

doi: 10.1371/journal.pone.0128036

Correspondence between BioAnalyzer traces and the length distribution of aligned reads. Panels A-C show three representative BioAnalyzer traces from three sample preparations of S . maltophilia . Panels D-F show the corresponding estimated fragment-size distributions (black) and the actual distributions of fragment lengths imputed from alignment to the reference genome (blue). A BioAnalyzer trace f(x) shows fluorescence f at fragment length x . However, we are interested in n(x) , the (relative) number of fragments n of length x . Since fluorescence of a DNA fragment is proportional to its length, n(x) ∝ f(x) / x . Note that sequencing can be successful despite the presence of apparently very long fragments (which are likely heteroduplexes) in the BioAnalyzer traces (Panels C and F).
Figure Legend Snippet: Correspondence between BioAnalyzer traces and the length distribution of aligned reads. Panels A-C show three representative BioAnalyzer traces from three sample preparations of S . maltophilia . Panels D-F show the corresponding estimated fragment-size distributions (black) and the actual distributions of fragment lengths imputed from alignment to the reference genome (blue). A BioAnalyzer trace f(x) shows fluorescence f at fragment length x . However, we are interested in n(x) , the (relative) number of fragments n of length x . Since fluorescence of a DNA fragment is proportional to its length, n(x) ∝ f(x) / x . Note that sequencing can be successful despite the presence of apparently very long fragments (which are likely heteroduplexes) in the BioAnalyzer traces (Panels C and F).

Techniques Used: Fluorescence, Sequencing

Dependence of fragment size distribution on input gDNA concentration and bead volume. DNA fragment size distribution is affected by starting genomic DNA concentration (rows) as described in Module 1 as well as the relative amount of bead buffer used in PCR clean-up (columns) as described in Module 4. Size distribution is measured by BioAnalyzer and reported in fluorescence units. Data is from Stenotrophomonas maltophilia (67% GC, 4.8 Mb genome). At high initial gDNA concentration (1.25 ng/μl) the fragment distribution is right-skewed, though this anomalous peak does not appear to significantly affect sequencing output.
Figure Legend Snippet: Dependence of fragment size distribution on input gDNA concentration and bead volume. DNA fragment size distribution is affected by starting genomic DNA concentration (rows) as described in Module 1 as well as the relative amount of bead buffer used in PCR clean-up (columns) as described in Module 4. Size distribution is measured by BioAnalyzer and reported in fluorescence units. Data is from Stenotrophomonas maltophilia (67% GC, 4.8 Mb genome). At high initial gDNA concentration (1.25 ng/μl) the fragment distribution is right-skewed, though this anomalous peak does not appear to significantly affect sequencing output.

Techniques Used: Concentration Assay, Polymerase Chain Reaction, Fluorescence, Sequencing

13) Product Images from "Unlocking Short Read Sequencing for Metagenomics"

Article Title: Unlocking Short Read Sequencing for Metagenomics

Journal: PLoS ONE

doi: 10.1371/journal.pone.0011840

Reproducibility of double-SPRI. The panel shows DNA fragment size distributions as obtained by Bioanalyzer DNA-1000 assays. The curves represent the size fractions removed during the first separation step A ) or recovered after the second separation B ). The two size fractions were independently reproduced in 4 or 8 separation experiments. The curves in B ) represent the libraries sequenced after dSPRI based size selection, adapter ligation and PCR enrichment. While concentrations (arbitrary fluorescence units) vary between reproduced libraries the range of removed or enriched DNA fragment sizes was highly reproducible. Panel c ) shows the DNA fragment size distribution recovered after the second separation when using decreasing amounts sheared genomic DNA. dSPRI allows reliable size selection in a DNA concentration independent manner.
Figure Legend Snippet: Reproducibility of double-SPRI. The panel shows DNA fragment size distributions as obtained by Bioanalyzer DNA-1000 assays. The curves represent the size fractions removed during the first separation step A ) or recovered after the second separation B ). The two size fractions were independently reproduced in 4 or 8 separation experiments. The curves in B ) represent the libraries sequenced after dSPRI based size selection, adapter ligation and PCR enrichment. While concentrations (arbitrary fluorescence units) vary between reproduced libraries the range of removed or enriched DNA fragment sizes was highly reproducible. Panel c ) shows the DNA fragment size distribution recovered after the second separation when using decreasing amounts sheared genomic DNA. dSPRI allows reliable size selection in a DNA concentration independent manner.

Techniques Used: Selection, Ligation, Polymerase Chain Reaction, Fluorescence, Concentration Assay

Size-dependent isolation of DNA fragments from sheared genomic DNA via dSPRI. AMPure XP SPRI beads bind DNA fragments in a size dependent manner according to the concentration of salts and polyethylene glycol (PEG) in the reaction [4] – [7] , which can easily be changed by using different volume ratios of DNA to SPRI bead solutions. A two-step procedure is employed to isolate targeted DNA size fractions. Panels A to H present Bioanalyzer DNA-1000 assays showing the sheared genomic DNA used as starting material (black), the larger size DNA fragments discarded in separation 1 (red), and the size fraction purified and recovered after separation 2 (blue). Panel I is a table summarizing the conditions and results displayed in panels A to H. All Bioanalyzer DNA-1000 traces after separation 1 (panel J), and after separation 2 (panel K), are respectively displayed on a graph for the conditions presented in panels A to H. The conditions displayed in panel H were used to obtaine the Illumina composite reads discussed in the text. The wider DNA fragment size distribution from panel H allowed to better analyze the effects of shorter versus longer overlapping regions on consensus reads.
Figure Legend Snippet: Size-dependent isolation of DNA fragments from sheared genomic DNA via dSPRI. AMPure XP SPRI beads bind DNA fragments in a size dependent manner according to the concentration of salts and polyethylene glycol (PEG) in the reaction [4] – [7] , which can easily be changed by using different volume ratios of DNA to SPRI bead solutions. A two-step procedure is employed to isolate targeted DNA size fractions. Panels A to H present Bioanalyzer DNA-1000 assays showing the sheared genomic DNA used as starting material (black), the larger size DNA fragments discarded in separation 1 (red), and the size fraction purified and recovered after separation 2 (blue). Panel I is a table summarizing the conditions and results displayed in panels A to H. All Bioanalyzer DNA-1000 traces after separation 1 (panel J), and after separation 2 (panel K), are respectively displayed on a graph for the conditions presented in panels A to H. The conditions displayed in panel H were used to obtaine the Illumina composite reads discussed in the text. The wider DNA fragment size distribution from panel H allowed to better analyze the effects of shorter versus longer overlapping regions on consensus reads.

Techniques Used: Isolation, Concentration Assay, Purification

14) Product Images from "Elucidation of a non-thermal mechanism for DNA/RNA fragmentation and protein degradation when using Lyse-It"

Article Title: Elucidation of a non-thermal mechanism for DNA/RNA fragmentation and protein degradation when using Lyse-It

Journal: PLoS ONE

doi: 10.1371/journal.pone.0225475

2100 high sensitivity DNA Bioanalyzer S . aureus . Bacteria were purged for 15 minutes and then lysed with Lyse-It for 30 seconds at 30% power (A and B) and 60 seconds at 50% power (C and D) . A and C) Total concentrations (pg/μL) below the reported base pairs. B and D) Concentrations (pg/μL) between base pair ranges.
Figure Legend Snippet: 2100 high sensitivity DNA Bioanalyzer S . aureus . Bacteria were purged for 15 minutes and then lysed with Lyse-It for 30 seconds at 30% power (A and B) and 60 seconds at 50% power (C and D) . A and C) Total concentrations (pg/μL) below the reported base pairs. B and D) Concentrations (pg/μL) between base pair ranges.

Techniques Used:

2100 high sensitivity DNA Bioanalyzer of V . cholerae . Bacteria were purged for 15 minutes and then lysed with Lyse-It for 30 seconds at 30% power. ( A and B) and 50% power, 60 seconds (C and D) Total concentrations (pg/μL) below the reported base pairs post 30% power, 30 seconds ( A) Concentrations (pg/μL) between base pair ranges for 30% power 30 seconds, (B) Total concentration before the reported base pairs post 50% power, 60 seconds (C) , and concentration between base pair ranges for 50% power, 60 seconds (D) .
Figure Legend Snippet: 2100 high sensitivity DNA Bioanalyzer of V . cholerae . Bacteria were purged for 15 minutes and then lysed with Lyse-It for 30 seconds at 30% power. ( A and B) and 50% power, 60 seconds (C and D) Total concentrations (pg/μL) below the reported base pairs post 30% power, 30 seconds ( A) Concentrations (pg/μL) between base pair ranges for 30% power 30 seconds, (B) Total concentration before the reported base pairs post 50% power, 60 seconds (C) , and concentration between base pair ranges for 50% power, 60 seconds (D) .

Techniques Used: Concentration Assay

15) Product Images from "Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line"

Article Title: Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line

Journal: Environmental Health

doi: 10.1186/1476-069X-11-31

Lymphoblasts were treated with NaAsO 2 at 0, 10, 20, 50 and 100 μM for two, four or eight hours. Levels of DNA methylation expressed as % of controls were illustrated as a dose-response and time-course study on global LINE-1 methylation determined by COBRA and quantified by capillary gel electrophoresis using a Bioanalyzer (A) , dose-response of arsenite treatment on total 5-MedC content determined by HPLC-MS/MS in lymphoblasts at four hours of treatment (B) and p53 promoter methylation in lymphoblasts treated with arsenite at 50 μM for four hours (C) . Each point represents the mean ± SE from three independent experiments. *,** and *** represent statistically significant difference from control at p
Figure Legend Snippet: Lymphoblasts were treated with NaAsO 2 at 0, 10, 20, 50 and 100 μM for two, four or eight hours. Levels of DNA methylation expressed as % of controls were illustrated as a dose-response and time-course study on global LINE-1 methylation determined by COBRA and quantified by capillary gel electrophoresis using a Bioanalyzer (A) , dose-response of arsenite treatment on total 5-MedC content determined by HPLC-MS/MS in lymphoblasts at four hours of treatment (B) and p53 promoter methylation in lymphoblasts treated with arsenite at 50 μM for four hours (C) . Each point represents the mean ± SE from three independent experiments. *,** and *** represent statistically significant difference from control at p

Techniques Used: DNA Methylation Assay, Methylation, Combined Bisulfite Restriction Analysis Assay, Nucleic Acid Electrophoresis, High Performance Liquid Chromatography, Mass Spectrometry

Lymphoblasts were treated with NaAsO 2 (0.0, 0.5 and 1.0 μM) for two up to eight weeks. The experiment was performed twice. Dose-response and time-course of arsenite treatment on levels of DNA methylation expressed as % of controls was determined as Global LINE-1 methylation determined by COBRA, quantified by capillary gel electrophoresis using a Bioanalyzer (A) , total 5-MedC content determined by HPLC-MS/MS (B) and p53 promoter methylation (C) . Each point represents the mean ± SE from three independent experiments. * and ** represent statistically significant difference from control at p
Figure Legend Snippet: Lymphoblasts were treated with NaAsO 2 (0.0, 0.5 and 1.0 μM) for two up to eight weeks. The experiment was performed twice. Dose-response and time-course of arsenite treatment on levels of DNA methylation expressed as % of controls was determined as Global LINE-1 methylation determined by COBRA, quantified by capillary gel electrophoresis using a Bioanalyzer (A) , total 5-MedC content determined by HPLC-MS/MS (B) and p53 promoter methylation (C) . Each point represents the mean ± SE from three independent experiments. * and ** represent statistically significant difference from control at p

Techniques Used: DNA Methylation Assay, Methylation, Combined Bisulfite Restriction Analysis Assay, Nucleic Acid Electrophoresis, High Performance Liquid Chromatography, Mass Spectrometry

16) Product Images from "Pathogens Inactivated by Low-Energy-Electron Irradiation Maintain Antigenic Properties and Induce Protective Immune Responses"

Article Title: Pathogens Inactivated by Low-Energy-Electron Irradiation Maintain Antigenic Properties and Induce Protective Immune Responses

Journal: Viruses

doi: 10.3390/v8110319

Characterization of the low-energy electron irradiation (LEEI) inactivated material. ( A ) Influenza A (H3N8) was LEEI-irradiated with the indicated doses (10 kGy, 20 kGy, and 30 kGy) or left non-irradiated (0 kGy) and RNA was isolated. Size and composition was analyzed by Agilent Bioanalyzer. The time scale on the X -axis represents the migration time in seconds, while FU represents the fluorescence intensity of the sample; ( B ) Median hemagglutination-units (HAU) of three independent experiments. HA-assay with LEEI-treated influenza A (H3N8)-material using chicken red blood cells in PBS. Non-irradiated (0 kGy) and irradiated (10 kGy, 30 kGy, and 50 kGy) samples were tested in triplicate. HA activity was measured as HAU and plotted as median with range; ( C ) Analysis of the antigen structure after inactivation by ELISA influenza A (H3N8) was inactivated by LEEI (30 kGy) or by adding formaldehyde either to a final concentration of 0.1% and incubation at 4 °C for 16 h (FA short), or to a final concentration of 0.05% followed by incubation at 37 °C for seven days (FA long). Untreated virus served as a positive control. Samples were coated on ELISA plates and probed with serum from an influenza A infected pig. Background was subtracted. Relative standard error of the mean (SEM) is indicated. p -values were determined by one-way ANOVA (*** p
Figure Legend Snippet: Characterization of the low-energy electron irradiation (LEEI) inactivated material. ( A ) Influenza A (H3N8) was LEEI-irradiated with the indicated doses (10 kGy, 20 kGy, and 30 kGy) or left non-irradiated (0 kGy) and RNA was isolated. Size and composition was analyzed by Agilent Bioanalyzer. The time scale on the X -axis represents the migration time in seconds, while FU represents the fluorescence intensity of the sample; ( B ) Median hemagglutination-units (HAU) of three independent experiments. HA-assay with LEEI-treated influenza A (H3N8)-material using chicken red blood cells in PBS. Non-irradiated (0 kGy) and irradiated (10 kGy, 30 kGy, and 50 kGy) samples were tested in triplicate. HA activity was measured as HAU and plotted as median with range; ( C ) Analysis of the antigen structure after inactivation by ELISA influenza A (H3N8) was inactivated by LEEI (30 kGy) or by adding formaldehyde either to a final concentration of 0.1% and incubation at 4 °C for 16 h (FA short), or to a final concentration of 0.05% followed by incubation at 37 °C for seven days (FA long). Untreated virus served as a positive control. Samples were coated on ELISA plates and probed with serum from an influenza A infected pig. Background was subtracted. Relative standard error of the mean (SEM) is indicated. p -values were determined by one-way ANOVA (*** p

Techniques Used: Irradiation, Isolation, Migration, Fluorescence, Hemagglutination Assay, Activity Assay, Enzyme-linked Immunosorbent Assay, Concentration Assay, Incubation, Positive Control, Infection

17) Product Images from "Viral latency locus augments B-cell response in vivo to induce chronic marginal zone enlargement, plasma cell hyperplasia, and lymphoma"

Article Title: Viral latency locus augments B-cell response in vivo to induce chronic marginal zone enlargement, plasma cell hyperplasia, and lymphoma

Journal: Blood

doi: 10.1182/blood-2012-03-415620

Transcription of KSHV miRNAs. (A) Transcription of pre-miRNAs and other transgenes was represented as RT-qPCR Ct values from 2 transgenic mice from 2 independent lines or a wild-type (WT) mouse. BC3, a PEL cell line, was used as a positive control. (B) Transcription of pre-miRNAs was validated using Bioanalyzer. RT+ and RT− represent RT-PCR reactions and reactions without reverse transcriptase, respectively. (C) Expression of mature miRNAs was confirmed using the TaqMan assay. Amplified products were visualized via the LabChip system. BC3, a PEL cell line was used as a positive control and U6 was used as a positive control for TaqMan assay system.
Figure Legend Snippet: Transcription of KSHV miRNAs. (A) Transcription of pre-miRNAs and other transgenes was represented as RT-qPCR Ct values from 2 transgenic mice from 2 independent lines or a wild-type (WT) mouse. BC3, a PEL cell line, was used as a positive control. (B) Transcription of pre-miRNAs was validated using Bioanalyzer. RT+ and RT− represent RT-PCR reactions and reactions without reverse transcriptase, respectively. (C) Expression of mature miRNAs was confirmed using the TaqMan assay. Amplified products were visualized via the LabChip system. BC3, a PEL cell line was used as a positive control and U6 was used as a positive control for TaqMan assay system.

Techniques Used: Quantitative RT-PCR, Transgenic Assay, Mouse Assay, Positive Control, Reverse Transcription Polymerase Chain Reaction, Expressing, TaqMan Assay, Amplification

18) Product Images from "Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples"

Article Title: Amplicon Sequencing of Colorectal Cancer: Variant Calling in Frozen and Formalin-Fixed Samples

Journal: PLoS ONE

doi: 10.1371/journal.pone.0127146

Depth of Sequencing correlates with DNA quality. (A) Sample preparation workflow. DNA was isolated from fresh frozen or FFPE CRC liver metastasis resection specimens with Qiagen Blood and Tissue or FFPE kit, respectively. Frozen samples then directly underwent sequencing library preparation, pooling of libraries, quality control and sequencing. FFPE samples were additionally tested for DNA quality by qPCR. Library quality was tested with Bioanalyzer. For samples with low amounts of correctly sized DNA amplicons (fragments at 310bp), new libraries were prepared with higher starting DNA concentrations and re-analyzed with Bioanalyzer. Samples with yet low amounts of DNA with correct size and highly fragmented DNA were excluded. (B) ΔCq-values of quality control PCR indicate poor sample quality. DNA concentration of fragments between 250bp and 450bp after library preparation was calculated with Agilent Bioanalyzer and plotted against ΔCq values of FFPE quality control PCR. (C) higher ΔCq-values correlate with lower mean depth of sequencing. (D) Coverage distribution of amplicons from all paired FFPE and frozen samples, normalized to total sample coverage. Frozen samples had a mean depth of 4,622, FFPE samples 1,852.
Figure Legend Snippet: Depth of Sequencing correlates with DNA quality. (A) Sample preparation workflow. DNA was isolated from fresh frozen or FFPE CRC liver metastasis resection specimens with Qiagen Blood and Tissue or FFPE kit, respectively. Frozen samples then directly underwent sequencing library preparation, pooling of libraries, quality control and sequencing. FFPE samples were additionally tested for DNA quality by qPCR. Library quality was tested with Bioanalyzer. For samples with low amounts of correctly sized DNA amplicons (fragments at 310bp), new libraries were prepared with higher starting DNA concentrations and re-analyzed with Bioanalyzer. Samples with yet low amounts of DNA with correct size and highly fragmented DNA were excluded. (B) ΔCq-values of quality control PCR indicate poor sample quality. DNA concentration of fragments between 250bp and 450bp after library preparation was calculated with Agilent Bioanalyzer and plotted against ΔCq values of FFPE quality control PCR. (C) higher ΔCq-values correlate with lower mean depth of sequencing. (D) Coverage distribution of amplicons from all paired FFPE and frozen samples, normalized to total sample coverage. Frozen samples had a mean depth of 4,622, FFPE samples 1,852.

Techniques Used: Sequencing, Sample Prep, Isolation, Formalin-fixed Paraffin-Embedded, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Concentration Assay

19) Product Images from "Isolation of intact RNA from murine CD4+ T cells after intracellular cytokine staining and fluorescence-activated cell sorting"

Article Title: Isolation of intact RNA from murine CD4+ T cells after intracellular cytokine staining and fluorescence-activated cell sorting

Journal: Journal of immunological methods

doi: 10.1016/j.jim.2018.02.008

Assessment of modified intracellular staining buffers. (A) Comparison of high salt buffer to standard permeabilization buffer (PB). Polyclonally stimulated splenocytes from C57BL/6 mice underwent ICS using two buffer conditions as indicated. Cells were then analyzed by flow cytometry and the expression of various cytokines by CD4 + for gating strategy. (B) Quality of RNA isolated from cells permeabilized with high salt buffer. CD4 + T cells were purified from naïve splenocytes, fixed with paraformaldehyde and permeabilized with high salt buffer. The cells were incubated for 16 hours in the same buffer before RNA isolation. Quality of isolated RNA was assessed by Agilent Bioanalyzer nano chips. nt, nucleotide, L, ladder; S, test sample. The number below the lane indicates corresponding RIN. (C) The experiments were performed as in Panel B except cells were permeabilized and incubated in permeabilization buffer containing RNase inhibitor. (D) CD4 + T cells isolated from naïve murine spleens underwent polyclonal stimulation and ICS staining for IFNγ using a permeabilization buffer containing RNase inhibitor. The cells were then analyzed with FACS Aria and IFNγ-producing CD4 + T cells were sorted into collection buffer containing 0.5 U/ml of RNase inhibitor. Quality of isolated RNA was assessed by Agilent Bioanalyzer pico chips which allows analysis of samples with low RNA concentration (0.05 – 5 ng/μl. s, seconds; L, ladder; S, test sample. The number below the lane indicates corresponding RIN. Results shown represent two independent experiments with n = 3 except the sorting experiments described in panel D which represents two independent experiments with n = 2.
Figure Legend Snippet: Assessment of modified intracellular staining buffers. (A) Comparison of high salt buffer to standard permeabilization buffer (PB). Polyclonally stimulated splenocytes from C57BL/6 mice underwent ICS using two buffer conditions as indicated. Cells were then analyzed by flow cytometry and the expression of various cytokines by CD4 + for gating strategy. (B) Quality of RNA isolated from cells permeabilized with high salt buffer. CD4 + T cells were purified from naïve splenocytes, fixed with paraformaldehyde and permeabilized with high salt buffer. The cells were incubated for 16 hours in the same buffer before RNA isolation. Quality of isolated RNA was assessed by Agilent Bioanalyzer nano chips. nt, nucleotide, L, ladder; S, test sample. The number below the lane indicates corresponding RIN. (C) The experiments were performed as in Panel B except cells were permeabilized and incubated in permeabilization buffer containing RNase inhibitor. (D) CD4 + T cells isolated from naïve murine spleens underwent polyclonal stimulation and ICS staining for IFNγ using a permeabilization buffer containing RNase inhibitor. The cells were then analyzed with FACS Aria and IFNγ-producing CD4 + T cells were sorted into collection buffer containing 0.5 U/ml of RNase inhibitor. Quality of isolated RNA was assessed by Agilent Bioanalyzer pico chips which allows analysis of samples with low RNA concentration (0.05 – 5 ng/μl. s, seconds; L, ladder; S, test sample. The number below the lane indicates corresponding RIN. Results shown represent two independent experiments with n = 3 except the sorting experiments described in panel D which represents two independent experiments with n = 2.

Techniques Used: Modification, Staining, Mouse Assay, Flow Cytometry, Cytometry, Expressing, Isolation, Purification, Incubation, FACS, Concentration Assay

20) Product Images from "Measuring Nucleosome Assembly Activity in vitro with the Nucleosome Assembly and Quantification (NAQ) Assay"

Article Title: Measuring Nucleosome Assembly Activity in vitro with the Nucleosome Assembly and Quantification (NAQ) Assay

Journal: Bio-protocol

doi: 10.21769/BioProtoc.2714

Example of output Bioanalyzer data of two samples Sample 1 (columns A–C). Sample 2 (columns E–G). Column I explains the interpreted nature of the bands identified.
Figure Legend Snippet: Example of output Bioanalyzer data of two samples Sample 1 (columns A–C). Sample 2 (columns E–G). Column I explains the interpreted nature of the bands identified.

Techniques Used:

Example of Bioanalyzer output data ).
Figure Legend Snippet: Example of Bioanalyzer output data ).

Techniques Used:

21) Product Images from "Coactosin-like protein 1 inhibits neuronal migration during mouse corticogenesis"

Article Title: Coactosin-like protein 1 inhibits neuronal migration during mouse corticogenesis

Journal: Journal of Veterinary Science

doi: 10.4142/jvs.2018.19.1.21

RNA bioanalyzer results for coactosin-like protein 1 (Cotl1) by the polymerase chain reaction. (A) Cotl1 RNA was expressed at a low level in specific periods in developing mouse cerebral cortex. (B) Internal reference (glyceraldehyde 3-phosphate dehydrogenase [GAPDH]) expression in mouse cerebral cortex. E, embryonic days; M, marker.
Figure Legend Snippet: RNA bioanalyzer results for coactosin-like protein 1 (Cotl1) by the polymerase chain reaction. (A) Cotl1 RNA was expressed at a low level in specific periods in developing mouse cerebral cortex. (B) Internal reference (glyceraldehyde 3-phosphate dehydrogenase [GAPDH]) expression in mouse cerebral cortex. E, embryonic days; M, marker.

Techniques Used: Polymerase Chain Reaction, Expressing, Marker

22) Product Images from "An Efficient LCM-Based Method for Tissue Specific Expression Analysis of Genes and miRNAs"

Article Title: An Efficient LCM-Based Method for Tissue Specific Expression Analysis of Genes and miRNAs

Journal: Scientific Reports

doi: 10.1038/srep21577

RNA isolation from LCM-derived tissue and the quality check using bio analyzer. (A) Embryonic RAM of Arabidopsis thaliana before (marked with red outline) and, (B) after LCM (C) Bioanalyzer-based analysis of LCM-tissue derived RNA. (Rep indicates replicate) using four different methods. RIN value shown for the result of each replicate indicates RNA quality.
Figure Legend Snippet: RNA isolation from LCM-derived tissue and the quality check using bio analyzer. (A) Embryonic RAM of Arabidopsis thaliana before (marked with red outline) and, (B) after LCM (C) Bioanalyzer-based analysis of LCM-tissue derived RNA. (Rep indicates replicate) using four different methods. RIN value shown for the result of each replicate indicates RNA quality.

Techniques Used: Isolation, Laser Capture Microdissection, Derivative Assay

23) Product Images from "Use of an Automated Multiple-Locus, Variable-Number Tandem Repeat-Based Method for Rapid and High-Throughput Genotyping of Staphylococcus aureus Isolates"

Article Title: Use of an Automated Multiple-Locus, Variable-Number Tandem Repeat-Based Method for Rapid and High-Throughput Genotyping of Staphylococcus aureus Isolates

Journal:

doi: 10.1128/JCM.43.7.3346-3355.2005

Comparison of electropherograms obtained for the strains sequenced. Representative electropherograms and the corresponding gel patterns (BioAnalyzer) obtained for strains MW2 and N315 are shown. Strain MW2 displays eight peaks, while strain N315 shows
Figure Legend Snippet: Comparison of electropherograms obtained for the strains sequenced. Representative electropherograms and the corresponding gel patterns (BioAnalyzer) obtained for strains MW2 and N315 are shown. Strain MW2 displays eight peaks, while strain N315 shows

Techniques Used:

Effect of lysis duration on DNA yields and PCR amplification results. (A) Amounts of total purified DNA obtained after the rapid lysis procedure (strain MW2), as determined by the fluorescence area under the curve (BioAnalyzer). The electropherogram shown
Figure Legend Snippet: Effect of lysis duration on DNA yields and PCR amplification results. (A) Amounts of total purified DNA obtained after the rapid lysis procedure (strain MW2), as determined by the fluorescence area under the curve (BioAnalyzer). The electropherogram shown

Techniques Used: Lysis, Polymerase Chain Reaction, Amplification, Purification, Fluorescence

24) Product Images from "An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries"

Article Title: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries

Journal: Scientific Reports

doi: 10.1038/srep37137

Quantitative evaluation of libraries prepared from oral gingival tissue. The quality of the libraries generated from gingival tissue was assessed after in vitro transcription and again after final cDNA synthesis. ( a ) Bioanalyzer (Agilent) trace showing the fragment size distributions for the six libraries after amplification by in vitro transcription. The traces from the automated protocol are shown in red while the traces from the manual protocol are shown in blue. The traces were also used to estimate the concentrations of the samples, which are illustrated in the left part of the boxplot ( c ). After the final cDNA synthesis the libraries were evaluated by quantitative PCR (qPCR) ( b ). The black vertical line marks the signal threshold at which point the cycle threshold (Ct) values were noted. The Ct values for the libraries as obtained from the qPCR are plotted in the right part of the boxplot ( c ).
Figure Legend Snippet: Quantitative evaluation of libraries prepared from oral gingival tissue. The quality of the libraries generated from gingival tissue was assessed after in vitro transcription and again after final cDNA synthesis. ( a ) Bioanalyzer (Agilent) trace showing the fragment size distributions for the six libraries after amplification by in vitro transcription. The traces from the automated protocol are shown in red while the traces from the manual protocol are shown in blue. The traces were also used to estimate the concentrations of the samples, which are illustrated in the left part of the boxplot ( c ). After the final cDNA synthesis the libraries were evaluated by quantitative PCR (qPCR) ( b ). The black vertical line marks the signal threshold at which point the cycle threshold (Ct) values were noted. The Ct values for the libraries as obtained from the qPCR are plotted in the right part of the boxplot ( c ).

Techniques Used: Generated, In Vitro, Amplification, Real-time Polymerase Chain Reaction

Quantitative evaluation of libraries prepared from total reference RNA. Sample-to-sample variation was investigated by small red triangles assessing the libraries at two points during the library preparation process. ( a ) The first evaluation is performed after in vitro transcription and checks the library concentrations and fragment lengths using a Bioanalyzer (Agilent). ( b ) After reverse transcription, a quantitative PCR (qPCR) was carried out to determine the suitable number of PCR cycles when indexing the finished libraries. The black vertical line marks the signal threshold at which point the cycle threshold (Ct) values were obtained. The spread of Ct values is illustrated in the boxplot ( c ), which also shows the variation in sample concentration as measured by the Bioanalyzer after in vitro transcription.
Figure Legend Snippet: Quantitative evaluation of libraries prepared from total reference RNA. Sample-to-sample variation was investigated by small red triangles assessing the libraries at two points during the library preparation process. ( a ) The first evaluation is performed after in vitro transcription and checks the library concentrations and fragment lengths using a Bioanalyzer (Agilent). ( b ) After reverse transcription, a quantitative PCR (qPCR) was carried out to determine the suitable number of PCR cycles when indexing the finished libraries. The black vertical line marks the signal threshold at which point the cycle threshold (Ct) values were obtained. The spread of Ct values is illustrated in the boxplot ( c ), which also shows the variation in sample concentration as measured by the Bioanalyzer after in vitro transcription.

Techniques Used: In Vitro, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Concentration Assay

25) Product Images from "mRNA-Seq of Single Prostate Cancer Circulating Tumor Cells Reveals Recapitulation of Gene Expression and Pathways Found in Prostate Cancer"

Article Title: mRNA-Seq of Single Prostate Cancer Circulating Tumor Cells Reveals Recapitulation of Gene Expression and Pathways Found in Prostate Cancer

Journal: PLoS ONE

doi: 10.1371/journal.pone.0049144

MagSweeper isolation has minimal effects on single cell transcriptomes. (A) Bioanalyzer traces of amplified cDNAs from single LNCaP cells pre (Single LNCaP(pre)) and post MagSweeping (Single LNCaP (post)), and positive control (12 pg of LNCaP total RNA) and negative control (Negative control). (B) Heatmap of correlations between fresh and MagSwept single-cell RNA-Seq data and table of correlations between fresh and MagSwept samples. Yellow indicates higher correlations and red lower correlations. (C) Representative bioanalyzer traces of good, intermediate, and poor CTC cDNA amplification products. (D) Percent breakout of CTC RNA quality based on classification of cDNA amplification products – green indicates good quality, yellow samples are partially degraded RNA and red indicates degraded RNA samples. (E) Sequenced CTCs, their RNA quality and % alignment of passing filter mRNA-Seq reads to the human genome build hg19. Patient CTC ID indicates single patient CTCs identified as patient number. CTC number (P1.1). RNA Quality is based on bioanalyzer traces of amplified cDNA and Align% is alignment % of mRNA-Seq reads.
Figure Legend Snippet: MagSweeper isolation has minimal effects on single cell transcriptomes. (A) Bioanalyzer traces of amplified cDNAs from single LNCaP cells pre (Single LNCaP(pre)) and post MagSweeping (Single LNCaP (post)), and positive control (12 pg of LNCaP total RNA) and negative control (Negative control). (B) Heatmap of correlations between fresh and MagSwept single-cell RNA-Seq data and table of correlations between fresh and MagSwept samples. Yellow indicates higher correlations and red lower correlations. (C) Representative bioanalyzer traces of good, intermediate, and poor CTC cDNA amplification products. (D) Percent breakout of CTC RNA quality based on classification of cDNA amplification products – green indicates good quality, yellow samples are partially degraded RNA and red indicates degraded RNA samples. (E) Sequenced CTCs, their RNA quality and % alignment of passing filter mRNA-Seq reads to the human genome build hg19. Patient CTC ID indicates single patient CTCs identified as patient number. CTC number (P1.1). RNA Quality is based on bioanalyzer traces of amplified cDNA and Align% is alignment % of mRNA-Seq reads.

Techniques Used: Isolation, Amplification, Positive Control, Negative Control, RNA Sequencing Assay

26) Product Images from "Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding"

Article Title: Profiling grapevine trunk pathogens in planta: a case for community-targeted DNA metabarcoding

Journal: BMC Microbiology

doi: 10.1186/s12866-018-1343-0

Primer design and testing. a Schematic representation of the annealing sites of forward and reverse GTAA, BITS, and SP primers in the fungal ribosal ITS. Reported amplicon sizes were calculated based on the ITS sequence of Eutypa lata (KU320617.1) as an example. b Bioanalyzer electropherograms showing PCR amplicons sizes generated using GTAA primers from purified fungal grapevine trunk pathogens: E. lata, Phaeoa. minimum, Dip. seriata, N. parvum , Phaeom. chlamydospora, and Dia. ampelina . Agrobacterium tumefaciens , V. vinifera and nuclease-free water were included as controls. c Bioanalyzer electropherograms showing PCR amplicons sizes generated using GTAA primers from selected field samples of mature vines infected with different trunk disease symptoms. AH: apparently healthy, ED: Eutypa Dieback, ES: Esca,WC: wood cankers (no leaf symptoms), and numbering corresponds to different biological replicates (same samples as in Fig. 5 ). d PCR products of GTAA, BITS, and SP primers from grapevine samples inoculated with N. parvum at six weeks post-inoculation sampled every five-cycles and visualized on an agarose gels. L: 100 bp Ladder. e Cycle thresholds (Ct) measured by qPCR of the same samples shown in ( d )
Figure Legend Snippet: Primer design and testing. a Schematic representation of the annealing sites of forward and reverse GTAA, BITS, and SP primers in the fungal ribosal ITS. Reported amplicon sizes were calculated based on the ITS sequence of Eutypa lata (KU320617.1) as an example. b Bioanalyzer electropherograms showing PCR amplicons sizes generated using GTAA primers from purified fungal grapevine trunk pathogens: E. lata, Phaeoa. minimum, Dip. seriata, N. parvum , Phaeom. chlamydospora, and Dia. ampelina . Agrobacterium tumefaciens , V. vinifera and nuclease-free water were included as controls. c Bioanalyzer electropherograms showing PCR amplicons sizes generated using GTAA primers from selected field samples of mature vines infected with different trunk disease symptoms. AH: apparently healthy, ED: Eutypa Dieback, ES: Esca,WC: wood cankers (no leaf symptoms), and numbering corresponds to different biological replicates (same samples as in Fig. 5 ). d PCR products of GTAA, BITS, and SP primers from grapevine samples inoculated with N. parvum at six weeks post-inoculation sampled every five-cycles and visualized on an agarose gels. L: 100 bp Ladder. e Cycle thresholds (Ct) measured by qPCR of the same samples shown in ( d )

Techniques Used: Amplification, Sequencing, Polymerase Chain Reaction, Generated, Purification, Infection, Real-time Polymerase Chain Reaction

27) Product Images from "Development of a fluorescent reporter system for monitoring ER stress in Chinese hamster ovary cells and its application for therapeutic protein production"

Article Title: Development of a fluorescent reporter system for monitoring ER stress in Chinese hamster ovary cells and its application for therapeutic protein production

Journal: PLoS ONE

doi: 10.1371/journal.pone.0183694

Expression analysis of UPR pathway proteins and monitoring with the RXG reporter in IgG-producing cell lines. (A) Splicing of the RXG reporter (sRXG) was determined by RTPCR followed by analysis using DNA 7500 chips with an Agilent Bioanalyzer. (B) Detection of key proteins involved in UPR by Western blot analysis. IRE1 pathway proteins XBP1 (uXBP1) and its spliced form (sXBP1), chaperones GRP94, BiP, PDI, P58 IPK , and PERK pathway proteins native PERK and eIF2α and their phosphorylated forms (p-PERK and p-eIF2α) were detected by Western blot analysis. GAPDH was used as a loading control. (C) Kinetics of QP and IVCC in IgG expressing cells during fed-batch culture. Threshold metrics for QP and IVCC critical for sustained inhibition of p-PERK are marked by dashed arrowed lines. (D) HC and LC mRNA expression of multiple RXG expressing stable IgG cell lines relative to GAPDH determined by qRTPCR. (E) Kinetics of ATF4 and CHOP mRNA expression during fed-batch culture of IgG expressing cells normalized on day 0 and expressed relative to endogenous GAPDH determined by real-time Q RTPCR. (F) Kinetics of ERAD and ERQC pathway proteins such as HERPUD1, (G) EDEM1 and Derlin1determined by real-time QRTPCR during fed-batch culture of IgG expressing cells.
Figure Legend Snippet: Expression analysis of UPR pathway proteins and monitoring with the RXG reporter in IgG-producing cell lines. (A) Splicing of the RXG reporter (sRXG) was determined by RTPCR followed by analysis using DNA 7500 chips with an Agilent Bioanalyzer. (B) Detection of key proteins involved in UPR by Western blot analysis. IRE1 pathway proteins XBP1 (uXBP1) and its spliced form (sXBP1), chaperones GRP94, BiP, PDI, P58 IPK , and PERK pathway proteins native PERK and eIF2α and their phosphorylated forms (p-PERK and p-eIF2α) were detected by Western blot analysis. GAPDH was used as a loading control. (C) Kinetics of QP and IVCC in IgG expressing cells during fed-batch culture. Threshold metrics for QP and IVCC critical for sustained inhibition of p-PERK are marked by dashed arrowed lines. (D) HC and LC mRNA expression of multiple RXG expressing stable IgG cell lines relative to GAPDH determined by qRTPCR. (E) Kinetics of ATF4 and CHOP mRNA expression during fed-batch culture of IgG expressing cells normalized on day 0 and expressed relative to endogenous GAPDH determined by real-time Q RTPCR. (F) Kinetics of ERAD and ERQC pathway proteins such as HERPUD1, (G) EDEM1 and Derlin1determined by real-time QRTPCR during fed-batch culture of IgG expressing cells.

Techniques Used: Expressing, Reverse Transcription Polymerase Chain Reaction, Western Blot, Inhibition

28) Product Images from "Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species"

Article Title: Human bone marrow- and adipose-mesenchymal stem cells secrete exosomes enriched in distinctive miRNA and tRNA species

Journal: Stem Cell Research & Therapy

doi: 10.1186/s13287-015-0116-z

ASCs and BMSCs contain relatively few MVBs and release exosome-like vesicles enriched in small RNAs. a Immunofluorescent staining of CD63 ( top left ) and EEA1 ( bottom left ), and ultrastructure of MVB-like endosomes ( right ) in ASCs and BMSCs. b Transmission electron microscopy micrographs of exosomes isolated from ASCs and BMSCs ( left ); and western blot for CD63, CD81, and cytochrome C in cells and corresponding exosomes ( right ). c Bioanalyzer small RNA profile of cells and exosomes showing enrichment of 20–70 nucleotide small RNAs in exosomes. ASC adipose-derived mesenchymal stem cell, BMSC bone marrow-derived mesenchymal stem cell, EEA1 early endosome antigen A1, exo exosome
Figure Legend Snippet: ASCs and BMSCs contain relatively few MVBs and release exosome-like vesicles enriched in small RNAs. a Immunofluorescent staining of CD63 ( top left ) and EEA1 ( bottom left ), and ultrastructure of MVB-like endosomes ( right ) in ASCs and BMSCs. b Transmission electron microscopy micrographs of exosomes isolated from ASCs and BMSCs ( left ); and western blot for CD63, CD81, and cytochrome C in cells and corresponding exosomes ( right ). c Bioanalyzer small RNA profile of cells and exosomes showing enrichment of 20–70 nucleotide small RNAs in exosomes. ASC adipose-derived mesenchymal stem cell, BMSC bone marrow-derived mesenchymal stem cell, EEA1 early endosome antigen A1, exo exosome

Techniques Used: Staining, Transmission Assay, Electron Microscopy, Isolation, Western Blot, Derivative Assay

29) Product Images from "Intrathecal delivery of frataxin mRNA encapsulated in lipid nanoparticles to dorsal root ganglia as a potential therapeutic for Friedreich’s ataxia"

Article Title: Intrathecal delivery of frataxin mRNA encapsulated in lipid nanoparticles to dorsal root ganglia as a potential therapeutic for Friedreich’s ataxia

Journal: Scientific Reports

doi: 10.1038/srep20019

FXN mRNA is translated and processed to yield mature functional FXN in transfected cells. ( A ) Schematic of the process used for mRNA generation. Linearized DNA template was used to generate the primary IVT product containing a cytomegalovirus (CMV) 5′ untranslated region (UTR) and a human growth hormone (hgh) 3′ UTR, and then subjected to 5′ capping and 3′ polyA tailing reactions to yield the final transcript. Bioanalyzer traces of IVT, capped product, and final polyA-tailed transcript are shown for ( A ) GFP and ( B ) FXN mRNA. ( C ) 293 T cells were transfected with the indicated amounts of FXN-6xHis or ( D ) FXN mRNA for 24 h before lysis and immunoblotting with the indicated antibodies. Anti-β-actin immunoblotting was used as a lane-loading control. p, i, and m indicate precursor, intermediate, and mature FXN protein immunopositive signals, respectively.
Figure Legend Snippet: FXN mRNA is translated and processed to yield mature functional FXN in transfected cells. ( A ) Schematic of the process used for mRNA generation. Linearized DNA template was used to generate the primary IVT product containing a cytomegalovirus (CMV) 5′ untranslated region (UTR) and a human growth hormone (hgh) 3′ UTR, and then subjected to 5′ capping and 3′ polyA tailing reactions to yield the final transcript. Bioanalyzer traces of IVT, capped product, and final polyA-tailed transcript are shown for ( A ) GFP and ( B ) FXN mRNA. ( C ) 293 T cells were transfected with the indicated amounts of FXN-6xHis or ( D ) FXN mRNA for 24 h before lysis and immunoblotting with the indicated antibodies. Anti-β-actin immunoblotting was used as a lane-loading control. p, i, and m indicate precursor, intermediate, and mature FXN protein immunopositive signals, respectively.

Techniques Used: Functional Assay, Transfection, Lysis

30) Product Images from "A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection"

Article Title: A Versatile Sample Processing Workflow for Metagenomic Pathogen Detection

Journal: Scientific Reports

doi: 10.1038/s41598-018-31496-1

Comparison of different disintegration methods. Shown is the RNA quality analysed using RNA 6000 Pico Chip (Bioanalyzer, Agilent). ( A ) Bacterial suspensions of exponentially growing Bacillus subtilis ( B . subtilis – EX) or endospores ( B . subtilis – SP), exponentially growing Staphylococcus aureus , or Escherichia coli ; ( B ) samples of swine faeces; ( C ) pools of midges. Legend: L, ladder; (−), without disintegration step; C, cryoPREP; M, Micro-Dismembrator; T, TissueLyser. The labelling for the ladder (fragment lengths, nucleotides) is given on the left side of each image.
Figure Legend Snippet: Comparison of different disintegration methods. Shown is the RNA quality analysed using RNA 6000 Pico Chip (Bioanalyzer, Agilent). ( A ) Bacterial suspensions of exponentially growing Bacillus subtilis ( B . subtilis – EX) or endospores ( B . subtilis – SP), exponentially growing Staphylococcus aureus , or Escherichia coli ; ( B ) samples of swine faeces; ( C ) pools of midges. Legend: L, ladder; (−), without disintegration step; C, cryoPREP; M, Micro-Dismembrator; T, TissueLyser. The labelling for the ladder (fragment lengths, nucleotides) is given on the left side of each image.

Techniques Used: Chromatin Immunoprecipitation

31) Product Images from "Translational reprogramming of colorectal cancer cells induced by 5-fluorouracil through a miRNA-dependent mechanism"

Article Title: Translational reprogramming of colorectal cancer cells induced by 5-fluorouracil through a miRNA-dependent mechanism

Journal: Oncotarget

doi: 10.18632/oncotarget.17597

Impact of 5-FU treatment on protein synthesis in HCT-116 cells (A-B) Global protein synthesis in response to 5-FU. Protein synthesis was quantified by 35 S labeling pulse-chase assays in non-treated and 5-FU treated cells. A representative gel is shown in (A) and mean quantification of three independent experiments is shown in (B). Compared to non-treated cells, a reproducible decrease in protein synthesis was observed in response to 10 μM of 5-FU for 24 hrs. Cycloheximide (CHX) was used as a positive control. (C-D) Polysome profiles in response to 5-FU. 40S and 60S ribosomal subunits, 80S monosomes and polysomes were separated by ultracentrifugation on sucrose gradients. One representative polysome profile of non-treated (C) and 10 μM 5-FU treated cells (D) is shown, as well as gel analysis of 18S and 28S rRNA used to verified RNA quality. On top of each profile, the fractions collected for microarray analyses (non-polysome NP and polysome P) are indicated. After RNA extraction, RNA quality was checked using bioanalyzer, the RNA Integrity Number (RIN) ranging from 6.6 to 9.3.
Figure Legend Snippet: Impact of 5-FU treatment on protein synthesis in HCT-116 cells (A-B) Global protein synthesis in response to 5-FU. Protein synthesis was quantified by 35 S labeling pulse-chase assays in non-treated and 5-FU treated cells. A representative gel is shown in (A) and mean quantification of three independent experiments is shown in (B). Compared to non-treated cells, a reproducible decrease in protein synthesis was observed in response to 10 μM of 5-FU for 24 hrs. Cycloheximide (CHX) was used as a positive control. (C-D) Polysome profiles in response to 5-FU. 40S and 60S ribosomal subunits, 80S monosomes and polysomes were separated by ultracentrifugation on sucrose gradients. One representative polysome profile of non-treated (C) and 10 μM 5-FU treated cells (D) is shown, as well as gel analysis of 18S and 28S rRNA used to verified RNA quality. On top of each profile, the fractions collected for microarray analyses (non-polysome NP and polysome P) are indicated. After RNA extraction, RNA quality was checked using bioanalyzer, the RNA Integrity Number (RIN) ranging from 6.6 to 9.3.

Techniques Used: Labeling, Pulse Chase, Positive Control, Microarray, RNA Extraction

32) Product Images from "Laser capture microdissection and genetic analysis of carbon-labeled Kupffer cells"

Article Title: Laser capture microdissection and genetic analysis of carbon-labeled Kupffer cells

Journal: World Journal of Gastroenterology : WJG

doi: 10.3748/wjg.15.1708

High quality RNA is extracted from material obtained by LCM. RNA size and quality were analyzed with the Agilent 2100 Bioanalyzer. A, B: Profiles of total RNA extracted from scrapes of the entire liver section (A) and from laser-captured cells (B); C: Electrophoresis gel of the same RNA.
Figure Legend Snippet: High quality RNA is extracted from material obtained by LCM. RNA size and quality were analyzed with the Agilent 2100 Bioanalyzer. A, B: Profiles of total RNA extracted from scrapes of the entire liver section (A) and from laser-captured cells (B); C: Electrophoresis gel of the same RNA.

Techniques Used: Laser Capture Microdissection, Electrophoresis

33) Product Images from "Laser Capture Microdissection in the Tissue Biorepository"

Article Title: Laser Capture Microdissection in the Tissue Biorepository

Journal: Journal of Biomolecular Techniques : JBT

doi:

The workflow of LCM. Tissue sections were cut using a cryostat or microtome and stained with hematoxylin and eosin (H E) for cell identification. Pure epithelial cell populations from frozen ovarian tissue were captured using the Arcturus XT LCM system and visualized on the LCM cap. Total RNA was then extracted, and the quantity and quality of RNA were monitored on an Agilent bioanalyzer. Two peaks, 18S and 28S ribosomal RNA, were obtained in the RNA profile generated by the bioanalyzer, indicating successful RNA sample isolation. The RNA was amplified for downstream analysis. QC, quality control; qPCR, quantitative PCR.
Figure Legend Snippet: The workflow of LCM. Tissue sections were cut using a cryostat or microtome and stained with hematoxylin and eosin (H E) for cell identification. Pure epithelial cell populations from frozen ovarian tissue were captured using the Arcturus XT LCM system and visualized on the LCM cap. Total RNA was then extracted, and the quantity and quality of RNA were monitored on an Agilent bioanalyzer. Two peaks, 18S and 28S ribosomal RNA, were obtained in the RNA profile generated by the bioanalyzer, indicating successful RNA sample isolation. The RNA was amplified for downstream analysis. QC, quality control; qPCR, quantitative PCR.

Techniques Used: Laser Capture Microdissection, Staining, Generated, Isolation, Amplification, Real-time Polymerase Chain Reaction

34) Product Images from "A method for high‐throughput production of sequence‐verified DNA libraries and strain collections"

Article Title: A method for high‐throughput production of sequence‐verified DNA libraries and strain collections

Journal: Molecular Systems Biology

doi: 10.15252/msb.20167233

Assembly of the mCherry gene from sequence‐verified fragments (1) First, 14 yeast clones containing sequence‐perfect fragments for assembly of mCherry were combined at equal concentrations and genomic DNA was isolated from this mixture. (2) From this genomic DNA, the 14 fragments were PCR‐amplified using common priming sites. Below each section, a bioanalyzer trace shows that the fragments were all of the appropriate size. (3) After PCR, the common priming sites were removed by digestion with BTSa1. (4) The digested fragments were then PCR‐assembled with primers that added homologies for vector integration, and size‐selected to obtain fragments of the appropriate size. (5) The assembled mCherry fragment was then inserted into a linearized expression vector by yeast homologous recombination. Expression of mCherry was confirmed by microscopy. Phase contrast (left) and mCherry (right) images for BY4743 cells and BY4743 cells carrying the mCherry plasmid are shown. Sanger sequencing confirmed perfect DNA sequence in six out of six clones.
Figure Legend Snippet: Assembly of the mCherry gene from sequence‐verified fragments (1) First, 14 yeast clones containing sequence‐perfect fragments for assembly of mCherry were combined at equal concentrations and genomic DNA was isolated from this mixture. (2) From this genomic DNA, the 14 fragments were PCR‐amplified using common priming sites. Below each section, a bioanalyzer trace shows that the fragments were all of the appropriate size. (3) After PCR, the common priming sites were removed by digestion with BTSa1. (4) The digested fragments were then PCR‐assembled with primers that added homologies for vector integration, and size‐selected to obtain fragments of the appropriate size. (5) The assembled mCherry fragment was then inserted into a linearized expression vector by yeast homologous recombination. Expression of mCherry was confirmed by microscopy. Phase contrast (left) and mCherry (right) images for BY4743 cells and BY4743 cells carrying the mCherry plasmid are shown. Sanger sequencing confirmed perfect DNA sequence in six out of six clones.

Techniques Used: Sequencing, Clone Assay, Isolation, Polymerase Chain Reaction, Amplification, Plasmid Preparation, Expressing, Homologous Recombination, Microscopy

35) Product Images from "Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types"

Article Title: Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types

Journal: Scientific Data

doi: 10.1038/sdata.2018.160

Quality control of the single cell sequencing library preparation. ( a ) Representative cDNA graphs from a validation plate, analyzed with a High Sensitivity D5000 ScreenTape on a TapeStation 4200. The size distribution of the cDNA was established by running a ladder (top left). A1 and A2 represent positive controls (20 cells), while P1 and P2 are empty negative controls. The other graphs display cDNA size distribution of randomly picked single cells of a validation plate after amplification. Graph E1 has colored boxes to assist in clarifying peak significance: Red boxes indicate upper and lower markers for size selection, the green box shows the cDNA size distribution and the blue box highlights the primer dimers. ( b ) Quality control of the pooled sequencing library after tagmentation with homemade Tn5 and indexing with the Nextera Indexing XT kit. The sequencing pools were analyzed on a BioAnalyzer with a High Sensitivity DNA Chip. Colored boxes describe peak significance as described above.
Figure Legend Snippet: Quality control of the single cell sequencing library preparation. ( a ) Representative cDNA graphs from a validation plate, analyzed with a High Sensitivity D5000 ScreenTape on a TapeStation 4200. The size distribution of the cDNA was established by running a ladder (top left). A1 and A2 represent positive controls (20 cells), while P1 and P2 are empty negative controls. The other graphs display cDNA size distribution of randomly picked single cells of a validation plate after amplification. Graph E1 has colored boxes to assist in clarifying peak significance: Red boxes indicate upper and lower markers for size selection, the green box shows the cDNA size distribution and the blue box highlights the primer dimers. ( b ) Quality control of the pooled sequencing library after tagmentation with homemade Tn5 and indexing with the Nextera Indexing XT kit. The sequencing pools were analyzed on a BioAnalyzer with a High Sensitivity DNA Chip. Colored boxes describe peak significance as described above.

Techniques Used: Sequencing, Amplification, Selection, Chromatin Immunoprecipitation

36) Product Images from "Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types"

Article Title: Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types

Journal: Scientific Data

doi: 10.1038/sdata.2018.160

Quality control of the single cell sequencing library preparation. ( a ) Representative cDNA graphs from a validation plate, analyzed with a High Sensitivity D5000 ScreenTape on a TapeStation 4200. The size distribution of the cDNA was established by running a ladder (top left). A1 and A2 represent positive controls (20 cells), while P1 and P2 are empty negative controls. The other graphs display cDNA size distribution of randomly picked single cells of a validation plate after amplification. Graph E1 has colored boxes to assist in clarifying peak significance: Red boxes indicate upper and lower markers for size selection, the green box shows the cDNA size distribution and the blue box highlights the primer dimers. ( b ) Quality control of the pooled sequencing library after tagmentation with homemade Tn5 and indexing with the Nextera Indexing XT kit. The sequencing pools were analyzed on a BioAnalyzer with a High Sensitivity DNA Chip. Colored boxes describe peak significance as described above.
Figure Legend Snippet: Quality control of the single cell sequencing library preparation. ( a ) Representative cDNA graphs from a validation plate, analyzed with a High Sensitivity D5000 ScreenTape on a TapeStation 4200. The size distribution of the cDNA was established by running a ladder (top left). A1 and A2 represent positive controls (20 cells), while P1 and P2 are empty negative controls. The other graphs display cDNA size distribution of randomly picked single cells of a validation plate after amplification. Graph E1 has colored boxes to assist in clarifying peak significance: Red boxes indicate upper and lower markers for size selection, the green box shows the cDNA size distribution and the blue box highlights the primer dimers. ( b ) Quality control of the pooled sequencing library after tagmentation with homemade Tn5 and indexing with the Nextera Indexing XT kit. The sequencing pools were analyzed on a BioAnalyzer with a High Sensitivity DNA Chip. Colored boxes describe peak significance as described above.

Techniques Used: Sequencing, Amplification, Selection, Chromatin Immunoprecipitation

37) Product Images from "Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types"

Article Title: Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types

Journal: Scientific Data

doi: 10.1038/sdata.2018.160

Quality control of the single cell sequencing library preparation. ( a ) Representative cDNA graphs from a validation plate, analyzed with a High Sensitivity D5000 ScreenTape on a TapeStation 4200. The size distribution of the cDNA was established by running a ladder (top left). A1 and A2 represent positive controls (20 cells), while P1 and P2 are empty negative controls. The other graphs display cDNA size distribution of randomly picked single cells of a validation plate after amplification. Graph E1 has colored boxes to assist in clarifying peak significance: Red boxes indicate upper and lower markers for size selection, the green box shows the cDNA size distribution and the blue box highlights the primer dimers. ( b ) Quality control of the pooled sequencing library after tagmentation with homemade Tn5 and indexing with the Nextera Indexing XT kit. The sequencing pools were analyzed on a BioAnalyzer with a High Sensitivity DNA Chip. Colored boxes describe peak significance as described above.
Figure Legend Snippet: Quality control of the single cell sequencing library preparation. ( a ) Representative cDNA graphs from a validation plate, analyzed with a High Sensitivity D5000 ScreenTape on a TapeStation 4200. The size distribution of the cDNA was established by running a ladder (top left). A1 and A2 represent positive controls (20 cells), while P1 and P2 are empty negative controls. The other graphs display cDNA size distribution of randomly picked single cells of a validation plate after amplification. Graph E1 has colored boxes to assist in clarifying peak significance: Red boxes indicate upper and lower markers for size selection, the green box shows the cDNA size distribution and the blue box highlights the primer dimers. ( b ) Quality control of the pooled sequencing library after tagmentation with homemade Tn5 and indexing with the Nextera Indexing XT kit. The sequencing pools were analyzed on a BioAnalyzer with a High Sensitivity DNA Chip. Colored boxes describe peak significance as described above.

Techniques Used: Sequencing, Amplification, Selection, Chromatin Immunoprecipitation

38) Product Images from "Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development"

Article Title: Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development

Journal: Bioinformatics

doi: 10.1093/bioinformatics/btx504

A typical bioanalyzer trace of total RNA from CFS isolated by the miRNeasy Micro Kit (Qiagen)
Figure Legend Snippet: A typical bioanalyzer trace of total RNA from CFS isolated by the miRNeasy Micro Kit (Qiagen)

Techniques Used: Isolation

39) Product Images from "The influence of rotor type and centrifugation time on the yield and purity of extracellular vesicles"

Article Title: The influence of rotor type and centrifugation time on the yield and purity of extracellular vesicles

Journal: Journal of Extracellular Vesicles

doi: 10.3402/jev.v3.23111

Alterations in the RNA profile during longer centrifugation duration. (A) RNase treatment of samples. Treated samples are presented as a percentage of RNA yield in comparison to yield of untreated control, which was kept on ice (red line marks 100%). (B) The RNA profile and yield of samples isolated with 70 minutes, 4 hours, 11 hours or a 37 hours centrifugation were determined with a Bioanalyzer. One representative experiment is shown per centrifugation time. (C) Profiles from B are shown in an overlay. Black arrows: 18 and 28 S ribosomal peaks; yellow dashed lines: 160–180 nt interval; blue dashed lines: 300–400 nt interval. (D) Ratios of the highest peak between 160 and 180 nt (yellow dashed lines in C) and the highest peak between 300 and 400 nt (blue dashed lines in C).
Figure Legend Snippet: Alterations in the RNA profile during longer centrifugation duration. (A) RNase treatment of samples. Treated samples are presented as a percentage of RNA yield in comparison to yield of untreated control, which was kept on ice (red line marks 100%). (B) The RNA profile and yield of samples isolated with 70 minutes, 4 hours, 11 hours or a 37 hours centrifugation were determined with a Bioanalyzer. One representative experiment is shown per centrifugation time. (C) Profiles from B are shown in an overlay. Black arrows: 18 and 28 S ribosomal peaks; yellow dashed lines: 160–180 nt interval; blue dashed lines: 300–400 nt interval. (D) Ratios of the highest peak between 160 and 180 nt (yellow dashed lines in C) and the highest peak between 300 and 400 nt (blue dashed lines in C).

Techniques Used: Centrifugation, Isolation

40) Product Images from "Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types"

Article Title: Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types

Journal: Scientific Data

doi: 10.1038/sdata.2018.160

Quality control of the single cell sequencing library preparation. ( a ) Representative cDNA graphs from a validation plate, analyzed with a High Sensitivity D5000 ScreenTape on a TapeStation 4200. The size distribution of the cDNA was established by running a ladder (top left). A1 and A2 represent positive controls (20 cells), while P1 and P2 are empty negative controls. The other graphs display cDNA size distribution of randomly picked single cells of a validation plate after amplification. Graph E1 has colored boxes to assist in clarifying peak significance: Red boxes indicate upper and lower markers for size selection, the green box shows the cDNA size distribution and the blue box highlights the primer dimers. ( b ) Quality control of the pooled sequencing library after tagmentation with homemade Tn5 and indexing with the Nextera Indexing XT kit. The sequencing pools were analyzed on a BioAnalyzer with a High Sensitivity DNA Chip. Colored boxes describe peak significance as described above.
Figure Legend Snippet: Quality control of the single cell sequencing library preparation. ( a ) Representative cDNA graphs from a validation plate, analyzed with a High Sensitivity D5000 ScreenTape on a TapeStation 4200. The size distribution of the cDNA was established by running a ladder (top left). A1 and A2 represent positive controls (20 cells), while P1 and P2 are empty negative controls. The other graphs display cDNA size distribution of randomly picked single cells of a validation plate after amplification. Graph E1 has colored boxes to assist in clarifying peak significance: Red boxes indicate upper and lower markers for size selection, the green box shows the cDNA size distribution and the blue box highlights the primer dimers. ( b ) Quality control of the pooled sequencing library after tagmentation with homemade Tn5 and indexing with the Nextera Indexing XT kit. The sequencing pools were analyzed on a BioAnalyzer with a High Sensitivity DNA Chip. Colored boxes describe peak significance as described above.

Techniques Used: Sequencing, Amplification, Selection, Chromatin Immunoprecipitation

41) Product Images from "Salivary extracellular vesicle-associated miRNAs as potential biomarkers in oral squamous cell carcinoma"

Article Title: Salivary extracellular vesicle-associated miRNAs as potential biomarkers in oral squamous cell carcinoma

Journal: BMC Cancer

doi: 10.1186/s12885-018-4364-z

Characterization of salivary EVs. ( a ) Representative NanoSight image of isolated EVs showing particle size (nm)/concentration (10^8 particles/ml) of a representative control (left) and a representative OSCC patient (right). ( b ) Representative transmission electron microscopy image of purified EVs negatively stained with NanoVan (JEOL Jem-1010 electron microscope, black line = 200 nm) of a control (left) and a patient (right). ( c ) Representative western blots confirming the expression of the exosome markers: CD63, CD9, Tsg101, and Alix, on salivary EVs from a control (left) and a OSCC patient (right). ( d ) Representative profiles of RNA isolated from EVs of a healthy control (left) and a patient (right). The graphs show fluorescence intensity [FU]/nucleotide length [nt] and were obtained through bioanalyzer analysis. Four experiments were performed with similar results
Figure Legend Snippet: Characterization of salivary EVs. ( a ) Representative NanoSight image of isolated EVs showing particle size (nm)/concentration (10^8 particles/ml) of a representative control (left) and a representative OSCC patient (right). ( b ) Representative transmission electron microscopy image of purified EVs negatively stained with NanoVan (JEOL Jem-1010 electron microscope, black line = 200 nm) of a control (left) and a patient (right). ( c ) Representative western blots confirming the expression of the exosome markers: CD63, CD9, Tsg101, and Alix, on salivary EVs from a control (left) and a OSCC patient (right). ( d ) Representative profiles of RNA isolated from EVs of a healthy control (left) and a patient (right). The graphs show fluorescence intensity [FU]/nucleotide length [nt] and were obtained through bioanalyzer analysis. Four experiments were performed with similar results

Techniques Used: Isolation, Concentration Assay, Transmission Assay, Electron Microscopy, Purification, Staining, Microscopy, Western Blot, Expressing, Fluorescence

42) Product Images from "Horizontal transfer of exosomal microRNAs transduce apoptotic signals between pancreatic beta-cells"

Article Title: Horizontal transfer of exosomal microRNAs transduce apoptotic signals between pancreatic beta-cells

Journal: Cell Communication and Signaling : CCS

doi: 10.1186/s12964-015-0097-7

Characterization of exosomes released by MIN6B1 cells. A) The sizes of microvesicles isolated by ultra-centrifugation from the culture media of MIN6B1 cells was measured using the Nanosight technology. B, C) Three different preparations of microvesicles from MIN6B1 cells were analyzed by immunoblotting for B) the presence of the exosomal protein markers Alix, CD81 and Tsg101, and C) for the absence of the cellular protein Calnexin. Cell extract was used as positive control for the detection of Calnexin. D) RNA profiles of MIN6B1 cells (upper panel) and of microvesicles (lower panel) were determined by Bioanalyzer.
Figure Legend Snippet: Characterization of exosomes released by MIN6B1 cells. A) The sizes of microvesicles isolated by ultra-centrifugation from the culture media of MIN6B1 cells was measured using the Nanosight technology. B, C) Three different preparations of microvesicles from MIN6B1 cells were analyzed by immunoblotting for B) the presence of the exosomal protein markers Alix, CD81 and Tsg101, and C) for the absence of the cellular protein Calnexin. Cell extract was used as positive control for the detection of Calnexin. D) RNA profiles of MIN6B1 cells (upper panel) and of microvesicles (lower panel) were determined by Bioanalyzer.

Techniques Used: Isolation, Centrifugation, Positive Control

43) Product Images from "Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens"

Article Title: Evaluation and Adaptation of a Laboratory-Based cDNA Library Preparation Protocol for Retrospective Sequencing of Archived MicroRNAs from up to 35-Year-Old Clinical FFPE Specimens

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms18030627

Evaluation of the optimized barcoded cDNA library preparation protocol with matched frozen and FFPE RNA samples. ( A ) Distance mapping of miRNA sequencing expression using the Euclidean distance metric for four pairs of matched frozen and FFPE specimens. Matched frozen (Fr-Cx) and eight-year-old FFPE (Ff-Cx) cervix tissue; matched frozen (Fr-Bngn) and four-year-old FFPE (Ff-Bngn) benign breast tissue; matched frozen (Fr-IBC1) and four-year-old FFPE (Ff-IBC1) invasive ductal carcinoma breast tissue #1; and matched frozen (Fr-IBC1) and eight-year-old FFPE (Ff-IBC2) invasive ductal carcinoma breast tissue #2 were analyzed; ( B ) RNA quality evaluation on a Bioanalyzer total RNA nano chip of matched frozen (Lanes 1 and 2) and FFPE (Lanes 3 and 4) IBC tissue pairs; ( C ) Scatter plot comparisons between matched frozen and FFPE IBC Tissues 1 and 2 (top right and left plots); ( D ) Correlation between IBC2/IBC1 fold-change in matched FFPE and frozen specimens, represented by abundance of miRNAs (log count per million (CPM), red to blue color) and significance of the expression difference between the two tissue pairs (Likelihood Ratio, values above 10 being significant ( p -value
Figure Legend Snippet: Evaluation of the optimized barcoded cDNA library preparation protocol with matched frozen and FFPE RNA samples. ( A ) Distance mapping of miRNA sequencing expression using the Euclidean distance metric for four pairs of matched frozen and FFPE specimens. Matched frozen (Fr-Cx) and eight-year-old FFPE (Ff-Cx) cervix tissue; matched frozen (Fr-Bngn) and four-year-old FFPE (Ff-Bngn) benign breast tissue; matched frozen (Fr-IBC1) and four-year-old FFPE (Ff-IBC1) invasive ductal carcinoma breast tissue #1; and matched frozen (Fr-IBC1) and eight-year-old FFPE (Ff-IBC2) invasive ductal carcinoma breast tissue #2 were analyzed; ( B ) RNA quality evaluation on a Bioanalyzer total RNA nano chip of matched frozen (Lanes 1 and 2) and FFPE (Lanes 3 and 4) IBC tissue pairs; ( C ) Scatter plot comparisons between matched frozen and FFPE IBC Tissues 1 and 2 (top right and left plots); ( D ) Correlation between IBC2/IBC1 fold-change in matched FFPE and frozen specimens, represented by abundance of miRNAs (log count per million (CPM), red to blue color) and significance of the expression difference between the two tissue pairs (Likelihood Ratio, values above 10 being significant ( p -value

Techniques Used: cDNA Library Assay, Formalin-fixed Paraffin-Embedded, Sequencing, Expressing, Chromatin Immunoprecipitation

44) Product Images from "Inhibition of stationary phase respiration impairs persister formation in E. coli"

Article Title: Inhibition of stationary phase respiration impairs persister formation in E. coli

Journal: Nature communications

doi: 10.1038/ncomms8983

RNA integrity, protein levels and degradation, and cells size of stationary phase cells ( A–C, E–F ) Cell cultures at early stationary phase (t=6 h) were treated with 1mM KCN or transferred to an anaerobic chamber. At t=24 h, cells were pelleted for RNA, protein, and microscope analyses. For controls, untreated overnight cultures (t=24 h) and early stationary phase cultures (t=6 h) were used. ( A–B ) RNA quality was determined with a bioanalyzer using an RNA 6000 Nano kit. The degradation of rRNA was assessed with RNA integrity values which range from 10 (intact) to 1 (totally degraded). (C) Cells were sonicated and the protein content in the supernatant was determined with Bradford assays. (D) Before KCN treatment at t=6 h, the inducer for gfp expression was removed in the cultures with the cells carrying pQE-80L gfp-ssrA . After the KCN treatment, GFP levels were measured. Background fluorescence was determined using cells with empty vectors. (E–F) Phase contrast images of fixed cells were taken using a microscope, and cell size (fold change relative to 24 h untreated overnight cultures) were determined with ImageJ. (G–H) KCN treatment was performed at t=9 h. At t=24 h, microscope images were taken, and ampicillin and ofloxacin persister levels were determined. * signifies significant differences for comparisons to control groups (p-value
Figure Legend Snippet: RNA integrity, protein levels and degradation, and cells size of stationary phase cells ( A–C, E–F ) Cell cultures at early stationary phase (t=6 h) were treated with 1mM KCN or transferred to an anaerobic chamber. At t=24 h, cells were pelleted for RNA, protein, and microscope analyses. For controls, untreated overnight cultures (t=24 h) and early stationary phase cultures (t=6 h) were used. ( A–B ) RNA quality was determined with a bioanalyzer using an RNA 6000 Nano kit. The degradation of rRNA was assessed with RNA integrity values which range from 10 (intact) to 1 (totally degraded). (C) Cells were sonicated and the protein content in the supernatant was determined with Bradford assays. (D) Before KCN treatment at t=6 h, the inducer for gfp expression was removed in the cultures with the cells carrying pQE-80L gfp-ssrA . After the KCN treatment, GFP levels were measured. Background fluorescence was determined using cells with empty vectors. (E–F) Phase contrast images of fixed cells were taken using a microscope, and cell size (fold change relative to 24 h untreated overnight cultures) were determined with ImageJ. (G–H) KCN treatment was performed at t=9 h. At t=24 h, microscope images were taken, and ampicillin and ofloxacin persister levels were determined. * signifies significant differences for comparisons to control groups (p-value

Techniques Used: Microscopy, Sonication, Expressing, Fluorescence, Significance Assay

45) Product Images from "High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics"

Article Title: High-throughput single-cell DNA sequencing of acute myeloid leukemia tumors with droplet microfluidics

Journal: Genome Research

doi: 10.1101/gr.232272.117

Protease-based workflows provide improved genomic DNA amplification. ( A ) When protease enzyme is left out of the workflow for single-cell gDNA PCR in droplets, only ∼5% of DU145 cells (viability stained on the x -axis) are positive for SRY TaqMan reaction fluorescence ( y -axis). Using protease during cell lysis improves the DU145 cell detection rate to ∼98% (red points in upper right quadrant). Points in the plot represent droplets. ( B ) Bioanalyzer traces of sequencing libraries prepared from cells processed through the workflow with (black trace) or without (red trace) the use of protease indicate that PCR amplification in droplets is improved with proteolysis. The two-step workflow with protease enables better sequencing coverage depth per cell across the eight amplified target loci listed on the x -axis ( C ).
Figure Legend Snippet: Protease-based workflows provide improved genomic DNA amplification. ( A ) When protease enzyme is left out of the workflow for single-cell gDNA PCR in droplets, only ∼5% of DU145 cells (viability stained on the x -axis) are positive for SRY TaqMan reaction fluorescence ( y -axis). Using protease during cell lysis improves the DU145 cell detection rate to ∼98% (red points in upper right quadrant). Points in the plot represent droplets. ( B ) Bioanalyzer traces of sequencing libraries prepared from cells processed through the workflow with (black trace) or without (red trace) the use of protease indicate that PCR amplification in droplets is improved with proteolysis. The two-step workflow with protease enables better sequencing coverage depth per cell across the eight amplified target loci listed on the x -axis ( C ).

Techniques Used: Amplification, Polymerase Chain Reaction, Staining, Fluorescence, Lysis, Sequencing

46) Product Images from "Bias in recent miRBase annotations potentially associated with RNA quality issues"

Article Title: Bias in recent miRBase annotations potentially associated with RNA quality issues

Journal: Scientific Reports

doi: 10.1038/s41598-017-05070-0

Experimental design. ( a ) Liver, heart and brain of male mice were harvested immediately after death, divided into 8 parts of about equal size, and stored at either 4 °C or at room temperature (RT) for the indicated time periods before RNA isolation. Experiments were performed in biological triplicates. RNA integrity was measured with Bioanalyzer. Gel-like image of brain tissue is given as example. MiRNA expression profiles of one replicate were measured using microarrays. ( b ) Liver tissue of 3 male mice was harvested immediately after death and divided into 5 parts of about equal size. Three parts were immediately transferred into RNAlater (0 h), two parts were stored for 96 h at room temperature (96 h). Two samples (0 h and 96 h) were isolated using standard procedure with miRNeasy Kit without DNase digestion. Two samples (0 h and 96 h) were isolated with optional DNase digestion to exclude DNA background. From the remaining undegraded sample (0 h), total RNA without small RNAs was isolated using RNeasy Kit with optional DNase digestion. Isolated RNA was further treated with 0 U, 0.026 U and 0.67 U RNase for 30 min to generate artificial RNA degradation. RNA integrity was measured with Bioanalyzer. MiRNA expression profiles of all replicates were measured using microarrays. The schematic drawings were prepared using the Biomedical-PPT-Toolkit-Suite from Motifolio Inc., USA.
Figure Legend Snippet: Experimental design. ( a ) Liver, heart and brain of male mice were harvested immediately after death, divided into 8 parts of about equal size, and stored at either 4 °C or at room temperature (RT) for the indicated time periods before RNA isolation. Experiments were performed in biological triplicates. RNA integrity was measured with Bioanalyzer. Gel-like image of brain tissue is given as example. MiRNA expression profiles of one replicate were measured using microarrays. ( b ) Liver tissue of 3 male mice was harvested immediately after death and divided into 5 parts of about equal size. Three parts were immediately transferred into RNAlater (0 h), two parts were stored for 96 h at room temperature (96 h). Two samples (0 h and 96 h) were isolated using standard procedure with miRNeasy Kit without DNase digestion. Two samples (0 h and 96 h) were isolated with optional DNase digestion to exclude DNA background. From the remaining undegraded sample (0 h), total RNA without small RNAs was isolated using RNeasy Kit with optional DNase digestion. Isolated RNA was further treated with 0 U, 0.026 U and 0.67 U RNase for 30 min to generate artificial RNA degradation. RNA integrity was measured with Bioanalyzer. MiRNA expression profiles of all replicates were measured using microarrays. The schematic drawings were prepared using the Biomedical-PPT-Toolkit-Suite from Motifolio Inc., USA.

Techniques Used: Mouse Assay, Isolation, Expressing

47) Product Images from "Revelation of mRNAs and proteins in porcine milk exosomes by transcriptomic and proteomic analysis"

Article Title: Revelation of mRNAs and proteins in porcine milk exosomes by transcriptomic and proteomic analysis

Journal: BMC Veterinary Research

doi: 10.1186/s12917-017-1021-8

Identification of proteins and mRNAs in porcine milk exosomes. a detection of the exosomal marker proteins CD63 and CD9 by Western blotting. b SDS-PAGE. c RNA sample analyzed by the Agilent Bioanalyzer 2100. d distribution of genen’s coverage
Figure Legend Snippet: Identification of proteins and mRNAs in porcine milk exosomes. a detection of the exosomal marker proteins CD63 and CD9 by Western blotting. b SDS-PAGE. c RNA sample analyzed by the Agilent Bioanalyzer 2100. d distribution of genen’s coverage

Techniques Used: Marker, Western Blot, SDS Page

48) Product Images from "Rapid, Dynamic Activation of Müller Glial Stem Cell Responses in Zebrafish"

Article Title: Rapid, Dynamic Activation of Müller Glial Stem Cell Responses in Zebrafish

Journal: Investigative Ophthalmology & Visual Science

doi: 10.1167/iovs.16-19973

Schematic representation of the Müller glia RNA-seq experimental design. ( A ) Photoreceptors were ablated in free-swimming Tg ( gfap:EGFP ) mi2002 fish using an acute light-lesion paradigm. ( B ) Retinas were dissected from unlesioned controls (0 hpl) and 8 and 16 hpl Tg ( gfap:EGFP ) mi2002 fish. Retinas were also dissected from unlesioned, wild-type (nontransgenic, GFP−) control fish. ( C ) Dissected retinas from each group were pooled and dissociated. ( D ) Dissociated samples were subjected to fluorescence-activated cell sorting (FACS), and GFP+ cells were collected. The FACS plots shown are representative images from the final gating and collection of actual samples. ( E ) RNA was isolated from the sorted cells and checked by Bioanalyzer for quality and concentration. Samples with an RNA integrity number (RIN) above 7.0 were advanced to library preparation. The Bioanalyzer electropherogram shown is a representative plot from an actual sample with a RIN of 8.6. The x -axis is in seconds, which corresponds to size. The y -axis shows fluorescent units (FU), corresponding to the amount of RNA. ( F ) RNA-seq libraries were prepared and checked again via Bioanalyzer. The Bioanalyzer electropherogram shown is a representative plot from a sample library preparation. The x -axis shows the size in base pairs. The y -axis shows fluorescent units, corresponding to the amount of DNA. ( G ) The RNA-seq libraries were then sequenced on an Illumina GAIIx. ( H ) The sequencing data were processed with bioinformatic tools for differential expression analysis, gene ontology analysis, and pathway analysis.
Figure Legend Snippet: Schematic representation of the Müller glia RNA-seq experimental design. ( A ) Photoreceptors were ablated in free-swimming Tg ( gfap:EGFP ) mi2002 fish using an acute light-lesion paradigm. ( B ) Retinas were dissected from unlesioned controls (0 hpl) and 8 and 16 hpl Tg ( gfap:EGFP ) mi2002 fish. Retinas were also dissected from unlesioned, wild-type (nontransgenic, GFP−) control fish. ( C ) Dissected retinas from each group were pooled and dissociated. ( D ) Dissociated samples were subjected to fluorescence-activated cell sorting (FACS), and GFP+ cells were collected. The FACS plots shown are representative images from the final gating and collection of actual samples. ( E ) RNA was isolated from the sorted cells and checked by Bioanalyzer for quality and concentration. Samples with an RNA integrity number (RIN) above 7.0 were advanced to library preparation. The Bioanalyzer electropherogram shown is a representative plot from an actual sample with a RIN of 8.6. The x -axis is in seconds, which corresponds to size. The y -axis shows fluorescent units (FU), corresponding to the amount of RNA. ( F ) RNA-seq libraries were prepared and checked again via Bioanalyzer. The Bioanalyzer electropherogram shown is a representative plot from a sample library preparation. The x -axis shows the size in base pairs. The y -axis shows fluorescent units, corresponding to the amount of DNA. ( G ) The RNA-seq libraries were then sequenced on an Illumina GAIIx. ( H ) The sequencing data were processed with bioinformatic tools for differential expression analysis, gene ontology analysis, and pathway analysis.

Techniques Used: RNA Sequencing Assay, Fluorescence In Situ Hybridization, Fluorescence, FACS, Isolation, Concentration Assay, Sequencing, Expressing

49) Product Images from "Cationic domains in particle-forming and assembly-deficient HBV core antigens capture mammalian RNA that stimulates Th1-biased antibody responses by DNA vaccination"

Article Title: Cationic domains in particle-forming and assembly-deficient HBV core antigens capture mammalian RNA that stimulates Th1-biased antibody responses by DNA vaccination

Journal: Scientific Reports

doi: 10.1038/s41598-018-32971-5

Expression and characterization of a mutant HBV-stC149tat antigen. ( a ) Schematic presentation of the HBV-stC149tat antigen. This antigen contained the HBV-stC149 sequence COOH-terminally fused with a 14-residue cationic HIV-tat 48–57 -like sequence. ( b–d ) 5 × 10 8 HEK-293 cells were transiently transfected with the pCI/stC149tat vector. The HBV-stC149tat fusion protein was purified from cell lysates using StrepTactin sepharose-packed columns. ( b ) 10 µl of the elution fractions 1-8 were processed SDS-PAGE analysis followed by Coomassie Blue staining of the gel. Molecular weight marker (in kDa) is shown. ( c ) Fractions with the highest antigen content were pooled and processed for native agarose gel electrophoresis followed by ethidium bromide (EB) and subsequent Coomassie Blue (CB) staining of the gel. The original gel used to generate this cropped figure is shown in Supplementary Fig. S3a . Purified HBV-stC149tat antigen was further analyzed by electron microscopy ( d ). The indicated scale bar represents 100 nm. ( e ) Purified HBV-stC149tat particles were incubated with proteinase K and remained either untreated or treated with RNase A or DNase. Samples were subjected to native agarose gel electrophoresis followed by ethidium bromide (EB)-staining of the gel. ( f ) The length profile of HEK-293 RNA isolated from non-treated cells (upper panel) or particle-bound RNA (lower panel) was analyzed on a Bioanalyzer 2100.
Figure Legend Snippet: Expression and characterization of a mutant HBV-stC149tat antigen. ( a ) Schematic presentation of the HBV-stC149tat antigen. This antigen contained the HBV-stC149 sequence COOH-terminally fused with a 14-residue cationic HIV-tat 48–57 -like sequence. ( b–d ) 5 × 10 8 HEK-293 cells were transiently transfected with the pCI/stC149tat vector. The HBV-stC149tat fusion protein was purified from cell lysates using StrepTactin sepharose-packed columns. ( b ) 10 µl of the elution fractions 1-8 were processed SDS-PAGE analysis followed by Coomassie Blue staining of the gel. Molecular weight marker (in kDa) is shown. ( c ) Fractions with the highest antigen content were pooled and processed for native agarose gel electrophoresis followed by ethidium bromide (EB) and subsequent Coomassie Blue (CB) staining of the gel. The original gel used to generate this cropped figure is shown in Supplementary Fig. S3a . Purified HBV-stC149tat antigen was further analyzed by electron microscopy ( d ). The indicated scale bar represents 100 nm. ( e ) Purified HBV-stC149tat particles were incubated with proteinase K and remained either untreated or treated with RNase A or DNase. Samples were subjected to native agarose gel electrophoresis followed by ethidium bromide (EB)-staining of the gel. ( f ) The length profile of HEK-293 RNA isolated from non-treated cells (upper panel) or particle-bound RNA (lower panel) was analyzed on a Bioanalyzer 2100.

Techniques Used: Expressing, Mutagenesis, Sequencing, Transfection, Plasmid Preparation, Purification, SDS Page, Staining, Molecular Weight, Marker, Agarose Gel Electrophoresis, Electron Microscopy, Incubation, Isolation

50) Product Images from "Cationic domains in particle-forming and assembly-deficient HBV core antigens capture mammalian RNA that stimulates Th1-biased antibody responses by DNA vaccination"

Article Title: Cationic domains in particle-forming and assembly-deficient HBV core antigens capture mammalian RNA that stimulates Th1-biased antibody responses by DNA vaccination

Journal: Scientific Reports

doi: 10.1038/s41598-018-32971-5

Expression and characterization of a mutant HBV-stC149tat antigen. ( a ) Schematic presentation of the HBV-stC149tat antigen. This antigen contained the HBV-stC149 sequence COOH-terminally fused with a 14-residue cationic HIV-tat 48–57 -like sequence. ( b–d ) 5 × 10 8 HEK-293 cells were transiently transfected with the pCI/stC149tat vector. The HBV-stC149tat fusion protein was purified from cell lysates using StrepTactin sepharose-packed columns. ( b ) 10 µl of the elution fractions 1-8 were processed SDS-PAGE analysis followed by Coomassie Blue staining of the gel. Molecular weight marker (in kDa) is shown. ( c . Purified HBV-stC149tat antigen was further analyzed by electron microscopy ( d ). The indicated scale bar represents 100 nm. ( e ) Purified HBV-stC149tat particles were incubated with proteinase K and remained either untreated or treated with RNase A or DNase. Samples were subjected to native agarose gel electrophoresis followed by ethidium bromide (EB)-staining of the gel. ( f ) The length profile of HEK-293 RNA isolated from non-treated cells (upper panel) or particle-bound RNA (lower panel) was analyzed on a Bioanalyzer 2100.
Figure Legend Snippet: Expression and characterization of a mutant HBV-stC149tat antigen. ( a ) Schematic presentation of the HBV-stC149tat antigen. This antigen contained the HBV-stC149 sequence COOH-terminally fused with a 14-residue cationic HIV-tat 48–57 -like sequence. ( b–d ) 5 × 10 8 HEK-293 cells were transiently transfected with the pCI/stC149tat vector. The HBV-stC149tat fusion protein was purified from cell lysates using StrepTactin sepharose-packed columns. ( b ) 10 µl of the elution fractions 1-8 were processed SDS-PAGE analysis followed by Coomassie Blue staining of the gel. Molecular weight marker (in kDa) is shown. ( c . Purified HBV-stC149tat antigen was further analyzed by electron microscopy ( d ). The indicated scale bar represents 100 nm. ( e ) Purified HBV-stC149tat particles were incubated with proteinase K and remained either untreated or treated with RNase A or DNase. Samples were subjected to native agarose gel electrophoresis followed by ethidium bromide (EB)-staining of the gel. ( f ) The length profile of HEK-293 RNA isolated from non-treated cells (upper panel) or particle-bound RNA (lower panel) was analyzed on a Bioanalyzer 2100.

Techniques Used: Expressing, Mutagenesis, Sequencing, Transfection, Plasmid Preparation, Purification, SDS Page, Staining, Molecular Weight, Marker, Electron Microscopy, Incubation, Agarose Gel Electrophoresis, Isolation

51) Product Images from "A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing"

Article Title: A Microfluidic DNA Library Preparation Platform for Next-Generation Sequencing

Journal: PLoS ONE

doi: 10.1371/journal.pone.0068988

Analysis of human gDNA at different stages of the Nextera protocol. Bioanalyzer traces of a) gDNA, b) post-tagmentation, c) post-limited-cycle PCR and d) post-size-selection. Peaks at 35 and 10380 bp represent low- and high-molecular weight markers.
Figure Legend Snippet: Analysis of human gDNA at different stages of the Nextera protocol. Bioanalyzer traces of a) gDNA, b) post-tagmentation, c) post-limited-cycle PCR and d) post-size-selection. Peaks at 35 and 10380 bp represent low- and high-molecular weight markers.

Techniques Used: Polymerase Chain Reaction, Selection, Molecular Weight

52) Product Images from "RNA sequencing data of Notch ligand treated human dental pulp cells"

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells

Journal: Data in Brief

doi: 10.1016/j.dib.2018.01.058

Quality check of input total RNA using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.
Figure Legend Snippet: Quality check of input total RNA using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.

Techniques Used:

53) Product Images from "Effects of aging and environmental tobacco smoke exposure on ocular and plasma circulatory microRNAs in the Rhesus macaque"

Article Title: Effects of aging and environmental tobacco smoke exposure on ocular and plasma circulatory microRNAs in the Rhesus macaque

Journal: Molecular Vision

doi:

Comparison of BioAnalyzer RNA profiles of circulatory microRNAs and small RNAs in Rhesus macaque ocular fluids and plasma. RNA profiles have the front labeled with a fluorescent marker (black arrow) and microRNA peak (red arrow): aqueous humor ( A ), vitreous humor ( B ), and plasma ( C ).
Figure Legend Snippet: Comparison of BioAnalyzer RNA profiles of circulatory microRNAs and small RNAs in Rhesus macaque ocular fluids and plasma. RNA profiles have the front labeled with a fluorescent marker (black arrow) and microRNA peak (red arrow): aqueous humor ( A ), vitreous humor ( B ), and plasma ( C ).

Techniques Used: Labeling, Marker

54) Product Images from "An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples"

Article Title: An Efficient Method for Identifying Gene Fusions by Targeted RNA Sequencing from Fresh Frozen and FFPE Samples

Journal: PLoS ONE

doi: 10.1371/journal.pone.0128916

HCC1937 Breast ductal carcinoma RNA. (A) FFPE RNA Bioanalyzer trace. (B) Bioanalyzer trace of sequencing library derived from 100 ng of RNA input shown in A. (C) Sequencing metrics for targeted RNA show that FFPE RNA is efficiently targeted.
Figure Legend Snippet: HCC1937 Breast ductal carcinoma RNA. (A) FFPE RNA Bioanalyzer trace. (B) Bioanalyzer trace of sequencing library derived from 100 ng of RNA input shown in A. (C) Sequencing metrics for targeted RNA show that FFPE RNA is efficiently targeted.

Techniques Used: Formalin-fixed Paraffin-Embedded, Sequencing, Derivative Assay

55) Product Images from "RNA sequencing data of Notch ligand treated human dental pulp cells"

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells

Journal: Data in Brief

doi: 10.1016/j.dib.2018.01.058

Quality check of input total RNA using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.
Figure Legend Snippet: Quality check of input total RNA using the Bioanalyzer. (A-C) hFc replicates; (D-F) Jagged1 replicates; (G-I) Jagged1+DAPT replicates.

Techniques Used:

56) Product Images from "Cancer-secreted AGR2 induces programmed cell death in normal cells"

Article Title: Cancer-secreted AGR2 induces programmed cell death in normal cells

Journal: Oncotarget

doi: 10.18632/oncotarget.9921

DNA fragmentation of AGR2-treated cells A. Bioanalyzer traces show the nucleic acid patterns of cultures listed on the top. The ribosomal RNA species are indicated. The left lane contains size standards. B. Traces show the patterns of necrotic NP strom cells. C. Traces compare the patterns of UV-irradiated (label 250 denotes 25 mJ/cm 2 ) NP strom cells and untreated cells. D. Traces show the time course of staurosporine treatment.
Figure Legend Snippet: DNA fragmentation of AGR2-treated cells A. Bioanalyzer traces show the nucleic acid patterns of cultures listed on the top. The ribosomal RNA species are indicated. The left lane contains size standards. B. Traces show the patterns of necrotic NP strom cells. C. Traces compare the patterns of UV-irradiated (label 250 denotes 25 mJ/cm 2 ) NP strom cells and untreated cells. D. Traces show the time course of staurosporine treatment.

Techniques Used: Irradiation

57) Product Images from "The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred"

Article Title: The mysterious Spotted Green Pigeon and its relation to the Dodo and its kindred

Journal: BMC Evolutionary Biology

doi: 10.1186/1471-2148-14-136

The Spotted Green Pigeon, extracted DNA characteristics and phylogeny. (A) Reconstruction of the Spotted Green or Liverpool Pigeon (courtesy of del Hoyo, J., Elliott, A., Sargatal, J. eds. 2002. Handbook of the Birds of the World. Vol. 7. Jacamars to Woodpeckers. Lynx Edicions, Barcelona), (B) a picture of the sole surviving specimen (courtesy of Clemency Fisher and the World Museum, National Museums Liverpool), (C) Bioanalyzer plot for the first DNA extract highlighting the short fragmentary nature of the DNA (median 51 bp). 35 bp and 10380 bp peaks are markers. FU: fluorescent units., (D) Maximum likelihood tree for the concatenated Spotted Green Pigeon sequences and 12S sequences from members of the extended Dodo clade (as identified by Shapiro et al. [ 1 ]) and (E) Maximum likelihood tree for 106 Pigeon mitochondrial 12S sequences. The Spotted Green Pigeon (bold) clusters first with the Nicobar Pigeon and second with the Dodo and Rodrigues Solitaire. Previously identified Pigeon clades in the phylogeny are coloured. The reason for the clustering of three rock Pigeon sequences ( Columba livia , grey box) with mourning doves ( Zenaida macroura ) is unclear, although hybridisation has been observed for these two species [ 5 ]. Bootstrap support values above 40 are indicated in the larger tree to allow for observation of the bootstrap value for the split between Caloenas and Raphinae, the dotted lines in both trees are there to associate the taxa with the appropriate tree tips.
Figure Legend Snippet: The Spotted Green Pigeon, extracted DNA characteristics and phylogeny. (A) Reconstruction of the Spotted Green or Liverpool Pigeon (courtesy of del Hoyo, J., Elliott, A., Sargatal, J. eds. 2002. Handbook of the Birds of the World. Vol. 7. Jacamars to Woodpeckers. Lynx Edicions, Barcelona), (B) a picture of the sole surviving specimen (courtesy of Clemency Fisher and the World Museum, National Museums Liverpool), (C) Bioanalyzer plot for the first DNA extract highlighting the short fragmentary nature of the DNA (median 51 bp). 35 bp and 10380 bp peaks are markers. FU: fluorescent units., (D) Maximum likelihood tree for the concatenated Spotted Green Pigeon sequences and 12S sequences from members of the extended Dodo clade (as identified by Shapiro et al. [ 1 ]) and (E) Maximum likelihood tree for 106 Pigeon mitochondrial 12S sequences. The Spotted Green Pigeon (bold) clusters first with the Nicobar Pigeon and second with the Dodo and Rodrigues Solitaire. Previously identified Pigeon clades in the phylogeny are coloured. The reason for the clustering of three rock Pigeon sequences ( Columba livia , grey box) with mourning doves ( Zenaida macroura ) is unclear, although hybridisation has been observed for these two species [ 5 ]. Bootstrap support values above 40 are indicated in the larger tree to allow for observation of the bootstrap value for the split between Caloenas and Raphinae, the dotted lines in both trees are there to associate the taxa with the appropriate tree tips.

Techniques Used: Hybridization

58) Product Images from "Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection"

Article Title: Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection

Journal: Silence

doi: 10.1186/1758-907X-3-9

Anticipated results. ( A ) Bioanalyzer plot. ( B ) Agarose gel for small-scale colony sequencing. Control, a PCR reaction with no bacterial colony added.
Figure Legend Snippet: Anticipated results. ( A ) Bioanalyzer plot. ( B ) Agarose gel for small-scale colony sequencing. Control, a PCR reaction with no bacterial colony added.

Techniques Used: Agarose Gel Electrophoresis, Sequencing, Polymerase Chain Reaction

59) Product Images from "Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification"

Article Title: Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkm1144

Yields obtained from amplification of different amounts of input DNA. An input DNA sample was obtained by reverse crosslinking chromatin extracts from a wild-type yeast culture, and used as starting material for a double-round T7 amplification. ( A ) Averaged RNA yields after two rounds of amplification are plotted as function of the amount of starting material used, which ranged from 0.4 to 2.5 ng. The concentration of T7 oligo added to the Klenow reactions was scaled proportionally with the amount of starting material, and set to 25 nM and 250 nM for the first and second round, respectively. Assays were performed in duplicate and error bars indicate the standard deviation. ( B ) Analysis of fragment size of amplified material after single round or double round of T7 amplification. One hundred and fifty nanograms of each sample was analyzed on an Agilent 2100 Bioanalyzer together with a RNA size marker. The fragment sizes of the RNA marker are indicated.
Figure Legend Snippet: Yields obtained from amplification of different amounts of input DNA. An input DNA sample was obtained by reverse crosslinking chromatin extracts from a wild-type yeast culture, and used as starting material for a double-round T7 amplification. ( A ) Averaged RNA yields after two rounds of amplification are plotted as function of the amount of starting material used, which ranged from 0.4 to 2.5 ng. The concentration of T7 oligo added to the Klenow reactions was scaled proportionally with the amount of starting material, and set to 25 nM and 250 nM for the first and second round, respectively. Assays were performed in duplicate and error bars indicate the standard deviation. ( B ) Analysis of fragment size of amplified material after single round or double round of T7 amplification. One hundred and fifty nanograms of each sample was analyzed on an Agilent 2100 Bioanalyzer together with a RNA size marker. The fragment sizes of the RNA marker are indicated.

Techniques Used: Amplification, Concentration Assay, Standard Deviation, Marker

60) Product Images from "A Biospecimen Proficiency Testing Program for Biobank Accreditation: Four Years of Experience"

Article Title: A Biospecimen Proficiency Testing Program for Biobank Accreditation: Four Years of Experience

Journal: Biopreservation and Biobanking

doi: 10.1089/bio.2015.0108

Evolution of Participants' performance in terms of z-scores after 1, 2, 3, or 4 years of participation in the (a) DNA Quantification and Purity Scheme (Assessment of DNA concentration by spectrophotometry), (b) DNA Quantification and Purity Scheme (Assessment of DNA 260/280 ratio by spectrophotometry), (c) RNA Integrity Scheme (Assessment of RNA Integrity using the Bioanalyzer).
Figure Legend Snippet: Evolution of Participants' performance in terms of z-scores after 1, 2, 3, or 4 years of participation in the (a) DNA Quantification and Purity Scheme (Assessment of DNA concentration by spectrophotometry), (b) DNA Quantification and Purity Scheme (Assessment of DNA 260/280 ratio by spectrophotometry), (c) RNA Integrity Scheme (Assessment of RNA Integrity using the Bioanalyzer).

Techniques Used: Concentration Assay, Spectrophotometry

61) Product Images from "Quantitative analysis of tRNA modifications by HPLC-coupled mass spectrometry"

Article Title: Quantitative analysis of tRNA modifications by HPLC-coupled mass spectrometry

Journal: Nature protocols

doi: 10.1038/nprot.2014.047

RNA quality control analysis on an Agilent Bioanalyzer. Total human TK6 cell RNA (red line) was resolved on a RNA Pico Chip in an Agilent 2100 Bioanalyzer. Size markers are noted in blue.
Figure Legend Snippet: RNA quality control analysis on an Agilent Bioanalyzer. Total human TK6 cell RNA (red line) was resolved on a RNA Pico Chip in an Agilent 2100 Bioanalyzer. Size markers are noted in blue.

Techniques Used: Chromatin Immunoprecipitation

62) Product Images from "Enterohemorrhagic Escherichia coli senses low biotin status in the large intestine for colonization and infection"

Article Title: Enterohemorrhagic Escherichia coli senses low biotin status in the large intestine for colonization and infection

Journal: Nature Communications

doi: 10.1038/ncomms7592

The effect of birA on the bacterial adherence capacity and the expression of biotin synthetic genes and LEE genes. ( a ) qRT–PCR quantification of changes in the expression of birA , bioA and bioB in O157 and O55 grown in DMEM supplemented with 0 or 100 nM biotin. ( b ) Adhesion of O157 WT, birA -, birA + and birA (over) to HeLa cells. ( c ) qRT–PCR quantification of changes in the expression of LEE genes in O157 WT, birA -, birA + and birA (over). ( d ) Adhesion of the O157 birA - strain to HeLa cells in DMEM supplemented with 0 or 100 nM biotin. ( e ) qRT–PCR quantification of the change in LEE gene expression in O157 birA - grown in DMEM supplemented with 0 or 100 nM biotin. ( f ) Adhesion of O55 WT, birA - and birA + to HeLa cells. ( g ) qRT–PCR was performed to measure the expression of LEE genes in O55 WT, birA - and birA +. ( h ) Immunoblot analysis of intimin and its receptor, Tir, in O157 WT, birA - and birA +. Full blots are shown in Supplementary Fig. 9 . birA -, birA mutant; birA +, birA -complemented strain; birA (over), birA -overexpression strain; WT, wild-type strain. Data are presented as means±s.d.; n =3. * P ≤0.05; ** P ≤0.01; *** P ≤0.001. All P values were calculated using Student’s t -test.
Figure Legend Snippet: The effect of birA on the bacterial adherence capacity and the expression of biotin synthetic genes and LEE genes. ( a ) qRT–PCR quantification of changes in the expression of birA , bioA and bioB in O157 and O55 grown in DMEM supplemented with 0 or 100 nM biotin. ( b ) Adhesion of O157 WT, birA -, birA + and birA (over) to HeLa cells. ( c ) qRT–PCR quantification of changes in the expression of LEE genes in O157 WT, birA -, birA + and birA (over). ( d ) Adhesion of the O157 birA - strain to HeLa cells in DMEM supplemented with 0 or 100 nM biotin. ( e ) qRT–PCR quantification of the change in LEE gene expression in O157 birA - grown in DMEM supplemented with 0 or 100 nM biotin. ( f ) Adhesion of O55 WT, birA - and birA + to HeLa cells. ( g ) qRT–PCR was performed to measure the expression of LEE genes in O55 WT, birA - and birA +. ( h ) Immunoblot analysis of intimin and its receptor, Tir, in O157 WT, birA - and birA +. Full blots are shown in Supplementary Fig. 9 . birA -, birA mutant; birA +, birA -complemented strain; birA (over), birA -overexpression strain; WT, wild-type strain. Data are presented as means±s.d.; n =3. * P ≤0.05; ** P ≤0.01; *** P ≤0.001. All P values were calculated using Student’s t -test.

Techniques Used: Expressing, Quantitative RT-PCR, Mutagenesis, Over Expression

63) Product Images from "The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing"

Article Title: The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing

Journal: Scientific Reports

doi: 10.1038/s41598-017-13887-y

RNA-sequencing analysis of three H3.3 WT and three H3.3 G34W primary cell lines show distinct splicing aberrations. ( a ) Electropherogram of MNase assay estimating chromatin compaction of mutated and unmutated primary cells. Plot based on 60 min incubation with MNase of H3.3 WT (blue line) and H3.3 G34W (red line) primary cell lines and BioAnalyzer data collection. ( b ) RNA splicing events of H3.3 G34W vs. H3.3 WT primary cells, extracted by the rMATS and SpliceR algorithms. The increased splicing events in H3.3 G34W when compared to H3.3 WT are given in [%]. ( c ) Plot of the significant increase of potentially novel isoforms. The data is based on the Cufflinks category j that calls for potentially novel isoforms (fragments) with at least one splice junction shared with a reference transcript. ( d ) Three examples (AURKA, NASP, and TPM2) of exon inclusion events in H3.3 G34W , first observed in RNA-seq. and here validated with the nCounter RNA-based hybridization technology. ( e ) Exon skipping in TUFT1 occur in H3.3 G34W , and probe detects junction of flanking exons to the skipped exon. ( f ) Alternative transcriptional start sites at the DDX10 and TPM1 locus. Increased read counts in their first or second introns indicated by red boxes. Plot of nCounter validations are shown in the right panel, where loss of normal start correlates with gain of alternative start.
Figure Legend Snippet: RNA-sequencing analysis of three H3.3 WT and three H3.3 G34W primary cell lines show distinct splicing aberrations. ( a ) Electropherogram of MNase assay estimating chromatin compaction of mutated and unmutated primary cells. Plot based on 60 min incubation with MNase of H3.3 WT (blue line) and H3.3 G34W (red line) primary cell lines and BioAnalyzer data collection. ( b ) RNA splicing events of H3.3 G34W vs. H3.3 WT primary cells, extracted by the rMATS and SpliceR algorithms. The increased splicing events in H3.3 G34W when compared to H3.3 WT are given in [%]. ( c ) Plot of the significant increase of potentially novel isoforms. The data is based on the Cufflinks category j that calls for potentially novel isoforms (fragments) with at least one splice junction shared with a reference transcript. ( d ) Three examples (AURKA, NASP, and TPM2) of exon inclusion events in H3.3 G34W , first observed in RNA-seq. and here validated with the nCounter RNA-based hybridization technology. ( e ) Exon skipping in TUFT1 occur in H3.3 G34W , and probe detects junction of flanking exons to the skipped exon. ( f ) Alternative transcriptional start sites at the DDX10 and TPM1 locus. Increased read counts in their first or second introns indicated by red boxes. Plot of nCounter validations are shown in the right panel, where loss of normal start correlates with gain of alternative start.

Techniques Used: RNA Sequencing Assay, Incubation, Hybridization

64) Product Images from "Transcriptome of Extracellular Vesicles Released by Hepatocytes"

Article Title: Transcriptome of Extracellular Vesicles Released by Hepatocytes

Journal: PLoS ONE

doi: 10.1371/journal.pone.0068693

Characterization of EVs. Characterization of EVs from MLP29 (A, C) and rat primary hepatocytes (RH) (B, D). The NTA analyses of two independent samples for each cell type show more heterogeneous vesicle populations released by primary culture of hepatocytes. Cryo-TEM pictures show membrane vesicles of different sizes (insets A–B). Bioanalyzer profiles of total RNA extracted by RNeasy from both cell types are similar with a wide distribution on size and also the presence of a reduced amount of ribosomal RNAs (C–D).
Figure Legend Snippet: Characterization of EVs. Characterization of EVs from MLP29 (A, C) and rat primary hepatocytes (RH) (B, D). The NTA analyses of two independent samples for each cell type show more heterogeneous vesicle populations released by primary culture of hepatocytes. Cryo-TEM pictures show membrane vesicles of different sizes (insets A–B). Bioanalyzer profiles of total RNA extracted by RNeasy from both cell types are similar with a wide distribution on size and also the presence of a reduced amount of ribosomal RNAs (C–D).

Techniques Used: Transmission Electron Microscopy

65) Product Images from "Identification of a Novel Oligodendrocyte Cell Adhesion Protein Using Gene Expression Profiling"

Article Title: Identification of a Novel Oligodendrocyte Cell Adhesion Protein Using Gene Expression Profiling

Journal: The Journal of neuroscience : the official journal of the Society for Neuroscience

doi: 10.1523/JNEUROSCI.2246-06.2006

Oligodendrocytes were purified directly from the whole brain of postnatal day 7 rats using flow cytometry. A , FACS density scatter plot in pseudocolor shows forward scatter (FSC) versus side scatter (SSC) properties used to identify viable cells (gate R1). B , A2B5 and O4 immunofluorescence signals were used in combination with gate R1 to sort-purify homogeneous populations of vital cells at early and later stages of oligodendrocyte differentiation. Gates were set to collect single A2B5 + progenitors expressing middle to high levels of A2B5 (top left quadrant, R2) and single O4 + oligodendrocytes (bottom right quadrant, R3). C , Agilent Bioanalyzer analysis of total RNA extracted from oligodendrocytes isolated by FACS demonstrates the intact 28S and 18S rRNA bands. D , Sorted A2B5 + cells cultured for 6 d differentiated into mature oligodendrocytes, as evidenced by strong immunoreactivity with the O1 antibody (red fluorescence). Scale bar, 10 μm.
Figure Legend Snippet: Oligodendrocytes were purified directly from the whole brain of postnatal day 7 rats using flow cytometry. A , FACS density scatter plot in pseudocolor shows forward scatter (FSC) versus side scatter (SSC) properties used to identify viable cells (gate R1). B , A2B5 and O4 immunofluorescence signals were used in combination with gate R1 to sort-purify homogeneous populations of vital cells at early and later stages of oligodendrocyte differentiation. Gates were set to collect single A2B5 + progenitors expressing middle to high levels of A2B5 (top left quadrant, R2) and single O4 + oligodendrocytes (bottom right quadrant, R3). C , Agilent Bioanalyzer analysis of total RNA extracted from oligodendrocytes isolated by FACS demonstrates the intact 28S and 18S rRNA bands. D , Sorted A2B5 + cells cultured for 6 d differentiated into mature oligodendrocytes, as evidenced by strong immunoreactivity with the O1 antibody (red fluorescence). Scale bar, 10 μm.

Techniques Used: Purification, Flow Cytometry, Cytometry, FACS, Immunofluorescence, Expressing, Isolation, Cell Culture, Fluorescence

66) Product Images from "Chemopreventive and Therapeutic Activity of Dietary Blueberry against Estrogen-Mediated Breast Cancer"

Article Title: Chemopreventive and Therapeutic Activity of Dietary Blueberry against Estrogen-Mediated Breast Cancer

Journal: Journal of Agricultural and Food Chemistry

doi: 10.1021/jf403734j

Expression of miRNAs 18a and 34c in mammary tissues. The small RNA was isolated by mirVana microRNA kit and quantified by Bioanalyzer. qPCR analysis was performed using a TaqMan microRNA Reverse Triscription Kit and TaqMan gene-specific MicroRNA assays. Graph represents the average of four rats ± SE done in duplicates. Asterisk indicates significant difference from E 2 -treated control ( p = 0.0013 and 0.0033).
Figure Legend Snippet: Expression of miRNAs 18a and 34c in mammary tissues. The small RNA was isolated by mirVana microRNA kit and quantified by Bioanalyzer. qPCR analysis was performed using a TaqMan microRNA Reverse Triscription Kit and TaqMan gene-specific MicroRNA assays. Graph represents the average of four rats ± SE done in duplicates. Asterisk indicates significant difference from E 2 -treated control ( p = 0.0013 and 0.0033).

Techniques Used: Expressing, Isolation, Real-time Polymerase Chain Reaction

67) Product Images from "Mapping RNA–RNA interactome and RNA structure in vivo by MARIO"

Article Title: Mapping RNA–RNA interactome and RNA structure in vivo by MARIO

Journal: Nature Communications

doi: 10.1038/ncomms12023

MARIO technology. ( a ) The major experimental steps are as follows: (1) cross-linking RNAs to proteins; (2) RNA fragmentation, protein denaturing and biotinylation; (3) immobilization of RNA-binding proteins at low density; (4) ligation of a biotinylated RNA linker; (5) proximity ligation under a dilute condition; (6) RNA purification and RT; (7) biotin pull-down; and (8) construction of sequencing library. ( b ) PCR validation of RNA1–Linker–RNA2 chimeras, which were expected to be above 91 bp from the P5 sequencing primer to the linker (purple) and above 200 bp from P5 to P7 sequencing primers. The failure to include RNA1 would create 91 bp products from P5 to the linker. The failure to include RNA2 would create similar-sized products from P5 to the linker and from P5 to P7. The PCR primers are marked on top of each lane. The size distribution of the sequencing libraries was also assessed by Bioanalyzer.
Figure Legend Snippet: MARIO technology. ( a ) The major experimental steps are as follows: (1) cross-linking RNAs to proteins; (2) RNA fragmentation, protein denaturing and biotinylation; (3) immobilization of RNA-binding proteins at low density; (4) ligation of a biotinylated RNA linker; (5) proximity ligation under a dilute condition; (6) RNA purification and RT; (7) biotin pull-down; and (8) construction of sequencing library. ( b ) PCR validation of RNA1–Linker–RNA2 chimeras, which were expected to be above 91 bp from the P5 sequencing primer to the linker (purple) and above 200 bp from P5 to P7 sequencing primers. The failure to include RNA1 would create 91 bp products from P5 to the linker. The failure to include RNA2 would create similar-sized products from P5 to the linker and from P5 to P7. The PCR primers are marked on top of each lane. The size distribution of the sequencing libraries was also assessed by Bioanalyzer.

Techniques Used: RNA Binding Assay, Ligation, Purification, Sequencing, Polymerase Chain Reaction

68) Product Images from "qPCR based mRNA quality score show intact mRNA after heat stabilization"

Article Title: qPCR based mRNA quality score show intact mRNA after heat stabilization

Journal: Biomolecular Detection and Quantification

doi: 10.1016/j.bdq.2016.01.002

Yield, quality and purity of extracted RNA (mean ± SD). Three different treatment groups, n = 4, (SF-snap frozen, HS-heat stabilized, HS + 12 h-heat stabilized with 12 h incubation at room temperature after heat stabilization), extracted with two different protocols (Q-QiaZol buffer and U + Q-Urea pre-solubilization prior to QiaZol extraction) were compared. μg RNA/mg tissue-yield of RNA from samples (left scale), RIN-RNA quality score as measured using the bioanalyzer (left scale), A260/A280-assesment of protein contamination (right scale), A260/A230-assesment of contaminants such as guanidine thiocynate and carbohydrates (right scale). * p
Figure Legend Snippet: Yield, quality and purity of extracted RNA (mean ± SD). Three different treatment groups, n = 4, (SF-snap frozen, HS-heat stabilized, HS + 12 h-heat stabilized with 12 h incubation at room temperature after heat stabilization), extracted with two different protocols (Q-QiaZol buffer and U + Q-Urea pre-solubilization prior to QiaZol extraction) were compared. μg RNA/mg tissue-yield of RNA from samples (left scale), RIN-RNA quality score as measured using the bioanalyzer (left scale), A260/A280-assesment of protein contamination (right scale), A260/A230-assesment of contaminants such as guanidine thiocynate and carbohydrates (right scale). * p

Techniques Used: Incubation

69) Product Images from "Identification of N6,N6-Dimethyladenosine in Transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin"

Article Title: Identification of N6,N6-Dimethyladenosine in Transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin

Journal: Molecules

doi: 10.3390/molecules16065168

Characterization of BCG small RNA species. An aliquot of small RNA isolated from BCG was analyzed on an Agilent Bioanalyzer small RNA chip. The peak at 4 nt in the electropherogram represents a size standard; the image on the right is the reconstructed gel image of the resolved RNA species.
Figure Legend Snippet: Characterization of BCG small RNA species. An aliquot of small RNA isolated from BCG was analyzed on an Agilent Bioanalyzer small RNA chip. The peak at 4 nt in the electropherogram represents a size standard; the image on the right is the reconstructed gel image of the resolved RNA species.

Techniques Used: Isolation, Chromatin Immunoprecipitation

70) Product Images from "Biobanking of Derivatives From Radical Retropubic and Robot-Assisted Laparoscopic Prostatectomy Tissues as Part of the Prostate Cancer Biorepository Network"

Article Title: Biobanking of Derivatives From Radical Retropubic and Robot-Assisted Laparoscopic Prostatectomy Tissues as Part of the Prostate Cancer Biorepository Network

Journal: The Prostate

doi: 10.1002/pros.22730

Assessment of nucleic acid quality as part of SOP development. A: Agarose gel of DNA samples extracted from frozen prostate tissue specimens. B: RIN of RNA samples extracted from frozen prostate tissues (Agilent Bioanalyzer). Mean RIN = 7.7 ±
Figure Legend Snippet: Assessment of nucleic acid quality as part of SOP development. A: Agarose gel of DNA samples extracted from frozen prostate tissue specimens. B: RIN of RNA samples extracted from frozen prostate tissues (Agilent Bioanalyzer). Mean RIN = 7.7 ±

Techniques Used: Agarose Gel Electrophoresis

71) Product Images from "Quantitative PCR analysis of laryngeal muscle fiber types"

Article Title: Quantitative PCR analysis of laryngeal muscle fiber types

Journal: Journal of communication disorders

doi: 10.1016/j.jcomdis.2010.04.006

Bioanalyzer output from total RNA extracted from soleus muscle diluted 10X (A) and 500X (B).
Figure Legend Snippet: Bioanalyzer output from total RNA extracted from soleus muscle diluted 10X (A) and 500X (B).

Techniques Used:

72) Product Images from "The histone chaperone FACT modulates nucleosome structure by tethering its components"

Article Title: The histone chaperone FACT modulates nucleosome structure by tethering its components

Journal: Life Science Alliance

doi: 10.26508/lsa.201800107

Nucleosomes assembled with FACT have similar MNase digestion pattern as salt-reconstituted nucleosomes. (A) 1 μM FACT was mixed with 250 nM (H3–H4) 2 tetramer and 500 nM H2A–H2B dimer and then 250 nM 207-bp 601 DNA was added. The supershifted FACT-containing complex was removed by M2 resin, and the flow through (containing various assembly products not bound by FACT) was collected for MNase digestion. (B) Protected DNA fragments were quantified using a Bioanalyzer. Nucleosomes assembled by FACT (red trace) have similar MNase digestion pattern compared with salt-reconstituted nucleosome (blue line). A different pattern is observed in the absence of FACT (mock sample, green line).
Figure Legend Snippet: Nucleosomes assembled with FACT have similar MNase digestion pattern as salt-reconstituted nucleosomes. (A) 1 μM FACT was mixed with 250 nM (H3–H4) 2 tetramer and 500 nM H2A–H2B dimer and then 250 nM 207-bp 601 DNA was added. The supershifted FACT-containing complex was removed by M2 resin, and the flow through (containing various assembly products not bound by FACT) was collected for MNase digestion. (B) Protected DNA fragments were quantified using a Bioanalyzer. Nucleosomes assembled by FACT (red trace) have similar MNase digestion pattern compared with salt-reconstituted nucleosome (blue line). A different pattern is observed in the absence of FACT (mock sample, green line).

Techniques Used: Flow Cytometry

Related Articles

Centrifugation:

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: DNA extraction was performed by adding 6 M NaCl to the solution, which was then vigorously shaken for 30 seconds prior to a 7 min centrifugation at 10,000xg. .. Prepared libraries (after PCRs amplification) were analyzed on a Bioanalyzer (Agilent, ) and 12 pM were loaded per lane into the sequencer.

Amplification:

Article Title: Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line
Article Snippet: The HpaII and MspI-digested DNA were amplified using p53 promoter region primers (F: 5’-AGGGAATTCGGCACCAGGTCGGGGAGA-3’ R: 5’-AGGATCGATGGACTCATCAAGTTCAGT-3’) for 31 cycles giving rise to a 341 bp PCR product. .. The PCR products (341 bp) were cleaned using a Qiagen MinElute purification kit prior to analysis with Bioanalyzer (Agilent).

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: .. Prepared libraries (after PCRs amplification) were analyzed on a Bioanalyzer (Agilent, ) and 12 pM were loaded per lane into the sequencer. ..

Article Title: Unlocking Short Read Sequencing for Metagenomics
Article Snippet: The amplified libraries were subjected to an additional round of AMPure XP SPRI beads purification, with a DNA/beads ratio of 1, to remove residual primers and adapter dimers. .. The samples were first analyzed using the High-Sensitivity DNA Kit for the Bioanalyzer (Agilent Technologies) to detect any primer-dimers and to determine the average molecular weight of each library.

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Article Snippet: The sense-RNA template library was prepared using 2.5 μg of fresh UHR RNA (Stratagene) and amplified using the SenseAmp RNA Amplification Kit from Genisphere, following the manufacturer's instructions. .. The integrity of the UHR-RNA was checked on a Bioanalyzer (Agilent).

Real-time Polymerase Chain Reaction:

Article Title: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Article Snippet: .. The libraries were evaluated during the preparation process using Bioanalyzer (Agilent) and qPCR ( ). .. Concentration measurements after in vitro transcription had a coefficient of variation (CV) of 57% for the manual samples and 1.5% for the automated samples.

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: All samples were analyzed with a Bioanalyzer (Agilent) DNA high-sensitive chip, which gives information on the size distribution ( B and ). .. This step is required for the accurate back calculation of molarity from qPCR and QuBit quantifications.

Article Title: Unlocking Short Read Sequencing for Metagenomics
Article Snippet: The samples were first analyzed using the High-Sensitivity DNA Kit for the Bioanalyzer (Agilent Technologies) to detect any primer-dimers and to determine the average molecular weight of each library. .. The samples were next quantified by real-time PCR on a LightCycler II 480 (Roche), using the LightCycler 480 SYBR Green I Master mix (Roche), appropriate primers , and serially diluted PhiX 335 bp control library (Illumina) as a standard (quantified with the Agilent Bioanalyzer; we observed that the Illumina PhiX 335 bp concentration vary from lot to lot, and typical concentrations were found to range from 11–15 nM).

Incubation:

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Article Snippet: The integrity of the UHR-RNA was checked on a Bioanalyzer (Agilent). .. The solution was incubated in a 0.5 μl microfuge PCR tube in a Perkin–Elmer Cetus DNA thermal cycler with a thermocycle file as follows: 70°C for 10 min, 70–42°C in 90 min.

Formalin-fixed Paraffin-Embedded:

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Article Snippet: For the restorations, the CT-RT process was performed using the single-stranded DNA primers obtained from 5 μg of FFPE-RNA from the 10-year-old breast cancer and the 3-year-old cervical samples. .. The integrity of the UHR-RNA was checked on a Bioanalyzer (Agilent).

Sequencing:

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells
Article Snippet: Paragraph title: RNA preparation and sequencing ... Further, RNA quality was examined using a bioanalyzer (Aligent 2100; Agilent Technologies, Santa Clara, CA, USA).

Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation
Article Snippet: For DNA inputs of 100 to 500 ng, libraries were pooled by volume (5 μl per sample; up to 96 samples) into a 1.5 mL tube prior to sequencing. .. Where described, library quality was determined by running 1 μl of the pooled library or an individual library on a Bioanalyzer (Agilent 2100 Bioanalyzer) using a High Sensitivity DNA kit (Agilent, cat. no. 5067–4626) or on a Fragment Analyzer (Advanced Analytical Fragment Analyzer) with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, cat. no. DNF-474).

Article Title: Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line
Article Snippet: PCR amplification of the sequence in region (638-978 bp) cannot be performed if one of the CCGG sequences has been cleaved. .. The PCR products (341 bp) were cleaned using a Qiagen MinElute purification kit prior to analysis with Bioanalyzer (Agilent).

Article Title: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Article Snippet: Comparing automated and manual preparations The automated protocol was benchmarked against the manual procedure by preparing and sequencing six libraries, which were obtained from adjacent sections in the same oral gingival tissue biopsy. .. The libraries were evaluated during the preparation process using Bioanalyzer (Agilent) and qPCR ( ).

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: After quantification (Nanodrop), 5 μg of DNA for each indexed library (n = 6) was used to prepare the NGS whole-genome sequencing assay following the manufacturer’s instructions (TruSeqTM Sample Prep Kit-v2, Illumina). .. Prepared libraries (after PCRs amplification) were analyzed on a Bioanalyzer (Agilent, ) and 12 pM were loaded per lane into the sequencer.

Article Title: Unlocking Short Read Sequencing for Metagenomics
Article Snippet: In order to achieve optimal cluster densities for sequencing on the Illumina GAII platform, samples were quantified using two methods. .. The samples were first analyzed using the High-Sensitivity DNA Kit for the Bioanalyzer (Agilent Technologies) to detect any primer-dimers and to determine the average molecular weight of each library.

Hi-C:

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: Prepared libraries (after PCRs amplification) were analyzed on a Bioanalyzer (Agilent, ) and 12 pM were loaded per lane into the sequencer. .. For high-resolution chromosome conformation capture (Hi-C) libraries , DNA was prepared using a previously published protocol .

Molecular Weight:

Article Title: Unlocking Short Read Sequencing for Metagenomics
Article Snippet: .. The samples were first analyzed using the High-Sensitivity DNA Kit for the Bioanalyzer (Agilent Technologies) to detect any primer-dimers and to determine the average molecular weight of each library. .. The samples were next quantified by real-time PCR on a LightCycler II 480 (Roche), using the LightCycler 480 SYBR Green I Master mix (Roche), appropriate primers , and serially diluted PhiX 335 bp control library (Illumina) as a standard (quantified with the Agilent Bioanalyzer; we observed that the Illumina PhiX 335 bp concentration vary from lot to lot, and typical concentrations were found to range from 11–15 nM).

DNA Extraction:

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: DNA extraction was performed by adding 6 M NaCl to the solution, which was then vigorously shaken for 30 seconds prior to a 7 min centrifugation at 10,000xg. .. Prepared libraries (after PCRs amplification) were analyzed on a Bioanalyzer (Agilent, ) and 12 pM were loaded per lane into the sequencer.

RNA Sequencing Assay:

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells
Article Snippet: Three biological replicates were employed in each group for RNA sequencing analysis. .. Further, RNA quality was examined using a bioanalyzer (Aligent 2100; Agilent Technologies, Santa Clara, CA, USA).

Methylation:

Article Title: Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line
Article Snippet: Paragraph title: Determination of p53 promoter methylation ... The PCR products (341 bp) were cleaned using a Qiagen MinElute purification kit prior to analysis with Bioanalyzer (Agilent).

Isolation:

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells
Article Snippet: RNA isolation was performed using an RNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol with DNaseI treatment. .. Further, RNA quality was examined using a bioanalyzer (Aligent 2100; Agilent Technologies, Santa Clara, CA, USA).

Article Title: Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination
Article Snippet: Paragraph title: Urine Exosome RNA Isolation Kit (lysis and column based; cited as Norgen) ... Next, 5 ng of bacterial RNA was mixed with 5 ng of cellular RNA and analyzed in Bioanalyzer (Agilent Technologies, Santa Clara, CA).

Article Title: Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model
Article Snippet: Paragraph title: Isolation of cfDNA from Human and Mouse Plasma/Serum ... Details of cfDNA purification are described in Section “Results.” All samples were analyzed using the bioanalyzer (Agilent, Santa Clara, CA, United States) to assess the distribution of cfDNA size using a high sensitivity DNA chip.

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells
Article Snippet: The concentration of the isolated RNAs ranged from 214.3–424.7 ng/μl. .. The RNA quality was further confirmed using a bioanalyzer (Aligent 2100; Agilent Technologies, Santa Clara, CA, USA).

Purification:

Article Title: Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line
Article Snippet: .. The PCR products (341 bp) were cleaned using a Qiagen MinElute purification kit prior to analysis with Bioanalyzer (Agilent). .. A sample of each amplified DNA (1 μl) was loaded onto a DNA chip according to the Agilent DNA 1000 kit protocol and assayed using the Bioanalyzer 2100 software.

Article Title: Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model
Article Snippet: .. Details of cfDNA purification are described in Section “Results.” All samples were analyzed using the bioanalyzer (Agilent, Santa Clara, CA, United States) to assess the distribution of cfDNA size using a high sensitivity DNA chip. .. Bisulfite Conversion, Library Construction, and Sequencing Bisulfite converted libraries were generated using the Zymo Research Pico Methyl-SeqTM Library Prep Kit (D5455).

Article Title: Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
Article Snippet: .. Materials and equipment Purified Nextera libraries from Module 4 High Sensitivity DNA kit for BioAnalyzer (Agilent 5067–4626) TE buffer 50mL reagent reservoirs 96-well plate with flat transparent bottom for fluorometry (e.g. Corning 3603) SYBR Green I (Life technologies S-7563) DNA standards in range of 1-10ng/μl (we use those that come with Life Q-33120) Plate reader with SYBR-compatible filters BioAnalyzer (Agilent 2100) or similar DNA fragment-size assay system. .. Procedure Perform steps 1–7 of Module 1 to quantify DNA concentration across all samples.

Article Title: Unlocking Short Read Sequencing for Metagenomics
Article Snippet: The amplified libraries were subjected to an additional round of AMPure XP SPRI beads purification, with a DNA/beads ratio of 1, to remove residual primers and adapter dimers. .. The samples were first analyzed using the High-Sensitivity DNA Kit for the Bioanalyzer (Agilent Technologies) to detect any primer-dimers and to determine the average molecular weight of each library.

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Article Snippet: We made one minor change to the procedure, by adding DNase-I prior to the sense-RNA purification in order to remove any trace of DNA. .. The integrity of the UHR-RNA was checked on a Bioanalyzer (Agilent).

Polymerase Chain Reaction:

Article Title: Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line
Article Snippet: .. The PCR products (341 bp) were cleaned using a Qiagen MinElute purification kit prior to analysis with Bioanalyzer (Agilent). .. A sample of each amplified DNA (1 μl) was loaded onto a DNA chip according to the Agilent DNA 1000 kit protocol and assayed using the Bioanalyzer 2100 software.

Article Title: Unlocking Short Read Sequencing for Metagenomics
Article Snippet: The resulting libraries were composed of fragments with distinct adapters at each extremities due to PCR suppression effect – . .. The samples were first analyzed using the High-Sensitivity DNA Kit for the Bioanalyzer (Agilent Technologies) to detect any primer-dimers and to determine the average molecular weight of each library.

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Article Snippet: The integrity of the UHR-RNA was checked on a Bioanalyzer (Agilent). .. The solution was incubated in a 0.5 μl microfuge PCR tube in a Perkin–Elmer Cetus DNA thermal cycler with a thermocycle file as follows: 70°C for 10 min, 70–42°C in 90 min.

Protein Extraction:

Article Title: Elucidation of a non-thermal mechanism for DNA/RNA fragmentation and protein degradation when using Lyse-It
Article Snippet: Oxygen concentration effect on DNA fragmentation of three bacteria–V . cholerae , L . monocytogenes , and S . aureus After the studies of protein extraction and degradation through conventional heating and microwave irradiation both with and without Lyse-It, it was important that DNA fragmentation also be investigated in varying oxygen concentrations. .. Any base pairs that were reported in the raw data of the Bioanalyzer below 35 bp and above 10000 bp were not used as those base pairs were the lower and upper markers of the Agilent High Sensitivity DNA kit.

Chloramphenicol Acetyltransferase Assay:

Article Title: Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model
Article Snippet: Isolation of cfDNA from Human and Mouse Plasma/Serum To isolate the cfDNA we utilized the Qiagen QIAamp Circulating Nucleic Acid kit (Cat no./ID: 55114) with the modifications described in Section “Results.” For cfDNA purification we compared Solid Phase Reversible Immobilisation beads (SPRI) from Beckman Coulter (Agencourt AMPure catA63880) with the DNA Clean & Concentrator kit, Zymo Research (D4003T). .. Details of cfDNA purification are described in Section “Results.” All samples were analyzed using the bioanalyzer (Agilent, Santa Clara, CA, United States) to assess the distribution of cfDNA size using a high sensitivity DNA chip.

Titration:

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: Paragraph title: NGS library titration ... All samples were analyzed with a Bioanalyzer (Agilent) DNA high-sensitive chip, which gives information on the size distribution ( B and ).

Chromatin Immunoprecipitation:

Article Title: Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line
Article Snippet: The PCR products (341 bp) were cleaned using a Qiagen MinElute purification kit prior to analysis with Bioanalyzer (Agilent). .. A sample of each amplified DNA (1 μl) was loaded onto a DNA chip according to the Agilent DNA 1000 kit protocol and assayed using the Bioanalyzer 2100 software.

Article Title: Development of a Method to Implement Whole-Genome Bisulfite Sequencing of cfDNA from Cancer Patients and a Mouse Tumor Model
Article Snippet: .. Details of cfDNA purification are described in Section “Results.” All samples were analyzed using the bioanalyzer (Agilent, Santa Clara, CA, United States) to assess the distribution of cfDNA size using a high sensitivity DNA chip. .. Bisulfite Conversion, Library Construction, and Sequencing Bisulfite converted libraries were generated using the Zymo Research Pico Methyl-SeqTM Library Prep Kit (D5455).

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: .. All samples were analyzed with a Bioanalyzer (Agilent) DNA high-sensitive chip, which gives information on the size distribution ( B and ). .. This step is required for the accurate back calculation of molarity from qPCR and QuBit quantifications.

SDS Page:

Article Title: Venom On-a-Chip: A Fast and Efficient Method for Comparative Venomics
Article Snippet: RP-HPLC Protein Fractions on the Bioanalyzer We tested the possibility of rapidly detecting the presence of specific toxin proteins using the Bioanalyzer as an alternative to SDS-PAGE gels. .. The same RP-HPLC fractions used for proteomic characterization were re-suspended in ddH2 O and run on the Bioanalyzer under reduced conditions using the Agilent Protein 80 kit.

Software:

Article Title: Effects of arsenic exposure on DNA methylation in cord blood samples from newborn babies and in a human lymphoblast cell line
Article Snippet: The PCR products (341 bp) were cleaned using a Qiagen MinElute purification kit prior to analysis with Bioanalyzer (Agilent). .. A sample of each amplified DNA (1 μl) was loaded onto a DNA chip according to the Agilent DNA 1000 kit protocol and assayed using the Bioanalyzer 2100 software.

SYBR Green Assay:

Article Title: Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes
Article Snippet: .. Materials and equipment Purified Nextera libraries from Module 4 High Sensitivity DNA kit for BioAnalyzer (Agilent 5067–4626) TE buffer 50mL reagent reservoirs 96-well plate with flat transparent bottom for fluorometry (e.g. Corning 3603) SYBR Green I (Life technologies S-7563) DNA standards in range of 1-10ng/μl (we use those that come with Life Q-33120) Plate reader with SYBR-compatible filters BioAnalyzer (Agilent 2100) or similar DNA fragment-size assay system. .. Procedure Perform steps 1–7 of Module 1 to quantify DNA concentration across all samples.

Article Title: Unlocking Short Read Sequencing for Metagenomics
Article Snippet: The samples were first analyzed using the High-Sensitivity DNA Kit for the Bioanalyzer (Agilent Technologies) to detect any primer-dimers and to determine the average molecular weight of each library. .. The samples were next quantified by real-time PCR on a LightCycler II 480 (Roche), using the LightCycler 480 SYBR Green I Master mix (Roche), appropriate primers , and serially diluted PhiX 335 bp control library (Illumina) as a standard (quantified with the Agilent Bioanalyzer; we observed that the Illumina PhiX 335 bp concentration vary from lot to lot, and typical concentrations were found to range from 11–15 nM).

RNA Extraction:

Article Title: Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination
Article Snippet: Bacteria isolated from urine were used for RNA extraction with Norgen Kit and assessed for quality and quantity. .. Next, 5 ng of bacterial RNA was mixed with 5 ng of cellular RNA and analyzed in Bioanalyzer (Agilent Technologies, Santa Clara, CA).

Sample Prep:

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: After quantification (Nanodrop), 5 μg of DNA for each indexed library (n = 6) was used to prepare the NGS whole-genome sequencing assay following the manufacturer’s instructions (TruSeqTM Sample Prep Kit-v2, Illumina). .. Prepared libraries (after PCRs amplification) were analyzed on a Bioanalyzer (Agilent, ) and 12 pM were loaded per lane into the sequencer.

In Vitro:

Article Title: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Article Snippet: The libraries were evaluated during the preparation process using Bioanalyzer (Agilent) and qPCR ( ). .. Concentration measurements after in vitro transcription had a coefficient of variation (CV) of 57% for the manual samples and 1.5% for the automated samples.

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Article Snippet: Paragraph title: T7 in vitro amplifications and CT-RT amplifications ... The integrity of the UHR-RNA was checked on a Bioanalyzer (Agilent).

Next-Generation Sequencing:

Article Title: Bead-linked transposomes enable a normalization-free workflow for NGS library preparation
Article Snippet: .. Where described, library quality was determined by running 1 μl of the pooled library or an individual library on a Bioanalyzer (Agilent 2100 Bioanalyzer) using a High Sensitivity DNA kit (Agilent, cat. no. 5067–4626) or on a Fragment Analyzer (Advanced Analytical Fragment Analyzer) with the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical, cat. no. DNF-474). ..

Article Title: Comparison of DNA Quantification Methods for Next Generation Sequencing
Article Snippet: Paragraph title: NGS library titration ... All samples were analyzed with a Bioanalyzer (Agilent) DNA high-sensitive chip, which gives information on the size distribution ( B and ).

Knock-Out:

Article Title: Molecular restoration of archived transcriptional profiles by complementary-template reverse-transcription (CT-RT)
Article Snippet: In order to prevent the T7-oligo dT(24) sequences of the purified cDNA primers from priming poly(A) sequences of random templates in the Sense-RNA template library, 1 μl of the Non-Sense Knock-out oligonucleotide (NSK), 5′-(A/C/T/G)(C/T/G)dA(24) CCGCCTCCCTATAGTGAGTCGTATTACAATTCACTGGCC-3′ (0.5 μg/μl was added to the 9 μl single-stranded cDNA solution. .. The integrity of the UHR-RNA was checked on a Bioanalyzer (Agilent).

Irradiation:

Article Title: Elucidation of a non-thermal mechanism for DNA/RNA fragmentation and protein degradation when using Lyse-It
Article Snippet: Oxygen concentration effect on DNA fragmentation of three bacteria–V . cholerae , L . monocytogenes , and S . aureus After the studies of protein extraction and degradation through conventional heating and microwave irradiation both with and without Lyse-It, it was important that DNA fragmentation also be investigated in varying oxygen concentrations. .. Any base pairs that were reported in the raw data of the Bioanalyzer below 35 bp and above 10000 bp were not used as those base pairs were the lower and upper markers of the Agilent High Sensitivity DNA kit.

Concentration Assay:

Article Title: RNA sequencing data of Notch ligand treated human dental pulp cells
Article Snippet: Further, RNA quality was examined using a bioanalyzer (Aligent 2100; Agilent Technologies, Santa Clara, CA, USA). .. The concentration of the isolated RNAs ranged from 214.3–424.7 ng/μl.

Article Title: An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries
Article Snippet: The libraries were evaluated during the preparation process using Bioanalyzer (Agilent) and qPCR ( ). .. Concentration measurements after in vitro transcription had a coefficient of variation (CV) of 57% for the manual samples and 1.5% for the automated samples.

Article Title: Elucidation of a non-thermal mechanism for DNA/RNA fragmentation and protein degradation when using Lyse-It
Article Snippet: Paragraph title: Oxygen concentration effect on DNA fragmentation of three bacteria–V . cholerae , L . monocytogenes , and S . aureus ... Any base pairs that were reported in the raw data of the Bioanalyzer below 35 bp and above 10000 bp were not used as those base pairs were the lower and upper markers of the Agilent High Sensitivity DNA kit.

Article Title: Unlocking Short Read Sequencing for Metagenomics
Article Snippet: The samples were first analyzed using the High-Sensitivity DNA Kit for the Bioanalyzer (Agilent Technologies) to detect any primer-dimers and to determine the average molecular weight of each library. .. The samples were next quantified by real-time PCR on a LightCycler II 480 (Roche), using the LightCycler 480 SYBR Green I Master mix (Roche), appropriate primers , and serially diluted PhiX 335 bp control library (Illumina) as a standard (quantified with the Agilent Bioanalyzer; we observed that the Illumina PhiX 335 bp concentration vary from lot to lot, and typical concentrations were found to range from 11–15 nM).

Lysis:

Article Title: Urinary extracellular vesicles for RNA extraction: optimization of a protocol devoid of prokaryote contamination
Article Snippet: Paragraph title: Urine Exosome RNA Isolation Kit (lysis and column based; cited as Norgen) ... Next, 5 ng of bacterial RNA was mixed with 5 ng of cellular RNA and analyzed in Bioanalyzer (Agilent Technologies, Santa Clara, CA).

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  • 99
    Agilent technologies agilent bioanalyzer
    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using <t>Agilent</t> <t>Bioanalyzer</t> 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.
    Agilent Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1974 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/agilent bioanalyzer/product/Agilent technologies
    Average 99 stars, based on 1974 article reviews
    Price from $9.99 to $1999.99
    agilent bioanalyzer - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    99
    Agilent technologies bioanalyzer
    Selected <t>bioanalyzer</t> electropherogram overlays from purified DNA (red) or 10% whole blood (blue). Results from five representative donors illustrate examples of a confirmed heterozyote (A) , heterozygote with a 10% blood under the default FU cutoff (B) , and suspected heterozygote with split peaks as an allelic differentiator and a larger artifact (C) , confirmed homozygote (D) , homozygote with two smaller artifacts (E) .
    Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 707 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioanalyzer/product/Agilent technologies
    Average 99 stars, based on 707 article reviews
    Price from $9.99 to $1999.99
    bioanalyzer - by Bioz Stars, 2020-01
    99/100 stars
      Buy from Supplier

    79
    Agilent technologies bioanalyzer shows overlaid electropherograms
    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent <t>Bioanalyzer</t> 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid <t>electropherograms</t> of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.
    Bioanalyzer Shows Overlaid Electropherograms, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 79/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioanalyzer shows overlaid electropherograms/product/Agilent technologies
    Average 79 stars, based on 4 article reviews
    Price from $9.99 to $1999.99
    bioanalyzer shows overlaid electropherograms - by Bioz Stars, 2020-01
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    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Analysis of effect of storage (22°C) on cfDNA in blood using Agilent Bioanalyzer The effect of blood storage at 22°C in K3 EDTA and ProTeck tubes on plasma DNA was studied using Agilent Bioanalyzer ( ). shows overlaid electropherograms of plasma cfDNA extracted from blood stored in K3 EDTA tubes at days 0, 3, 7, 14 and 28.

    Techniques:

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 30°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 2, 3, 7 and 14. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 2, 3, 7 and 14. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 30°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 2, 3, 7 and 14. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 2, 3, 7 and 14. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Analysis of effect of storage (22°C) on cfDNA in blood using Agilent Bioanalyzer The effect of blood storage at 22°C in K3 EDTA and ProTeck tubes on plasma DNA was studied using Agilent Bioanalyzer ( ). shows overlaid electropherograms of plasma cfDNA extracted from blood stored in K3 EDTA tubes at days 0, 3, 7, 14 and 28.

    Techniques:

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 4°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 3, 7, 14 and 21. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 3, 7, 14 and 21. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 4°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 3, 7, 14 and 21. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 3, 7, 14 and 21. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Analysis of effect of storage (22°C) on cfDNA in blood using Agilent Bioanalyzer The effect of blood storage at 22°C in K3 EDTA and ProTeck tubes on plasma DNA was studied using Agilent Bioanalyzer ( ). shows overlaid electropherograms of plasma cfDNA extracted from blood stored in K3 EDTA tubes at days 0, 3, 7, 14 and 28.

    Techniques:

    Selected bioanalyzer electropherogram overlays from purified DNA (red) or 10% whole blood (blue). Results from five representative donors illustrate examples of a confirmed heterozyote (A) , heterozygote with a 10% blood under the default FU cutoff (B) , and suspected heterozygote with split peaks as an allelic differentiator and a larger artifact (C) , confirmed homozygote (D) , homozygote with two smaller artifacts (E) .

    Journal: BMC Medical Genetics

    Article Title: PCR amplification of a triple-repeat genetic target directly from whole blood in 15 minutes as a proof-of-principle PCR study for direct sample analysis for a clinically relevant target

    doi: 10.1186/s12881-014-0130-5

    Figure Lengend Snippet: Selected bioanalyzer electropherogram overlays from purified DNA (red) or 10% whole blood (blue). Results from five representative donors illustrate examples of a confirmed heterozyote (A) , heterozygote with a 10% blood under the default FU cutoff (B) , and suspected heterozygote with split peaks as an allelic differentiator and a larger artifact (C) , confirmed homozygote (D) , homozygote with two smaller artifacts (E) .

    Article Snippet: Bioanalyzer sample analysis was carried out using the Agilent 1000 DNA kit (Catalog No.: 5067–1504) as per manufacturer’s specifications.

    Techniques: Purification

    Rapid PCR screening of DM1 with Agilent bioanalyzer detection. 10 ng purified donor DNA (P) or 10% direct whole blood (B) from 40 numerically-indicated donors with detection using the Agilent 2100 Bioanalyzer DNA 1000 kit. N (no template control); M (marker; the 200 to 100 base pair range is indicated).

    Journal: BMC Medical Genetics

    Article Title: PCR amplification of a triple-repeat genetic target directly from whole blood in 15 minutes as a proof-of-principle PCR study for direct sample analysis for a clinically relevant target

    doi: 10.1186/s12881-014-0130-5

    Figure Lengend Snippet: Rapid PCR screening of DM1 with Agilent bioanalyzer detection. 10 ng purified donor DNA (P) or 10% direct whole blood (B) from 40 numerically-indicated donors with detection using the Agilent 2100 Bioanalyzer DNA 1000 kit. N (no template control); M (marker; the 200 to 100 base pair range is indicated).

    Article Snippet: Bioanalyzer sample analysis was carried out using the Agilent 1000 DNA kit (Catalog No.: 5067–1504) as per manufacturer’s specifications.

    Techniques: Polymerase Chain Reaction, Purification, Marker

    DM1 screening using the Gene Link Genemer Kit with Agilent bioanalyzer detection. 100 ng purified donor DNA (P) from 40 numerically-indicated donors with detection using the Agilent 2100 Bioanalyzer DNA 1000 kit. N (no template control); M (marker; the 200 to 100 base pair range is indicated).

    Journal: BMC Medical Genetics

    Article Title: PCR amplification of a triple-repeat genetic target directly from whole blood in 15 minutes as a proof-of-principle PCR study for direct sample analysis for a clinically relevant target

    doi: 10.1186/s12881-014-0130-5

    Figure Lengend Snippet: DM1 screening using the Gene Link Genemer Kit with Agilent bioanalyzer detection. 100 ng purified donor DNA (P) from 40 numerically-indicated donors with detection using the Agilent 2100 Bioanalyzer DNA 1000 kit. N (no template control); M (marker; the 200 to 100 base pair range is indicated).

    Article Snippet: Bioanalyzer sample analysis was carried out using the Agilent 1000 DNA kit (Catalog No.: 5067–1504) as per manufacturer’s specifications.

    Techniques: Purification, Marker

    Selected bioanalyzer electropherogram overlays from purified DNA (red) using the Gene Link Myotonic Dystrophy Genemer Kit. Results from five representative donors illustrate examples of a confirmed heterozyote (A) , heterozygote with a 10% blood under the default FU cutoff (B) , and suspected heterozygote with split peaks as an allelic differentiator and a larger artifact (C) , confirmed homozygote (D) , homozygote with two smaller artifacts (E) .

    Journal: BMC Medical Genetics

    Article Title: PCR amplification of a triple-repeat genetic target directly from whole blood in 15 minutes as a proof-of-principle PCR study for direct sample analysis for a clinically relevant target

    doi: 10.1186/s12881-014-0130-5

    Figure Lengend Snippet: Selected bioanalyzer electropherogram overlays from purified DNA (red) using the Gene Link Myotonic Dystrophy Genemer Kit. Results from five representative donors illustrate examples of a confirmed heterozyote (A) , heterozygote with a 10% blood under the default FU cutoff (B) , and suspected heterozygote with split peaks as an allelic differentiator and a larger artifact (C) , confirmed homozygote (D) , homozygote with two smaller artifacts (E) .

    Article Snippet: Bioanalyzer sample analysis was carried out using the Agilent 1000 DNA kit (Catalog No.: 5067–1504) as per manufacturer’s specifications.

    Techniques: Purification

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 22°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in K 3 EDTA tubes at days 0, 3, 7, 14 and 28. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored (at 22°C) in ProTeck tubes at days 0, 3, 7, 14 and 28. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Analysis of effect of storage (4°C) on cfDNA in blood using Agilent Bioanalyzer shows overlaid electropherograms and Bioanalyzer gel of plasma cfDNA extracted from blood stored in K3 EDTA tubes, respectively.

    Techniques:

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 30°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 2, 3, 7 and 14. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 2, 3, 7 and 14. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 30°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 2, 3, 7 and 14. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 2, 3, 7 and 14. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Analysis of effect of storage (4°C) on cfDNA in blood using Agilent Bioanalyzer shows overlaid electropherograms and Bioanalyzer gel of plasma cfDNA extracted from blood stored in K3 EDTA tubes, respectively.

    Techniques:

    Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 4°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 3, 7, 14 and 21. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 3, 7, 14 and 21. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Journal: PLoS ONE

    Article Title: A novel approach to stabilize fetal cell-free DNA fraction in maternal blood samples for extended period of time

    doi: 10.1371/journal.pone.0208508

    Figure Lengend Snippet: Analysis of plasma cfDNA obtained from one representative pregnant donor blood stored at 4°C using Agilent Bioanalyzer 2100 instrument and Agilent DNA high sensitivity Kit. A, Overlaid electropherograms of plasma cfDNA extracted from blood stored in K 3 EDTA tubes at days 0, 3, 7, 14 and 21. B, Overlaid electropherograms of plasma cfDNA extracted from blood stored in ProTeck tubes at days 0, 3, 7, 14 and 21. C, Bioanalyzer gel image for blood stored in K 3 EDTA tubes. D, Bioanalyzer gel image for blood stored in ProTeck tubes. Cell-free DNA obtained from 3 pregnant donors were analyzed. This figure shows only the results of one representative pregnant donor.

    Article Snippet: Analysis of effect of storage (4°C) on cfDNA in blood using Agilent Bioanalyzer shows overlaid electropherograms and Bioanalyzer gel of plasma cfDNA extracted from blood stored in K3 EDTA tubes, respectively.

    Techniques: