Structured Review

Agilent technologies bioanalyzer 2100
Electropherograms obtained with the <t>Bioanalyzer</t> 2100 in miRNA-Ref and plasma samples. Examples of the profiles obtained from a miRNA-Ref sample at 10 ng/μL ( a , Bio-PicoChip; ( b ), Bio-SmallChip), a miRNA-Ref sample at 1 ng/μL ( c , Bio-PicoChip; ( d ), Bio-SmallChip), and a plasma sample ( e , Bio-PicoChip; ( f ), Bio-SmallChip). The 10 ng/µL miRNA-Ref sample ( a ) was diluted to fit the detection range of the Bio-PicoChip (0.05–5 ng/µL) and the final concentration was calculated by applying the dilution factor to the value obtained by the Bioanalyzer. In the miRNA-Ref samples ( a – d ), the overall profile is consistent with the presence of ribosomic RNA enriched with small RNAs, whereas in plasma samples ( e , f ) only small RNAs, but no long RNAs, are present. All electropherograms include the corresponding quantification (in bold) and the RNA integrity number (RIN) number (in italics) obtained with the Bio-PicoChip ( a , c , e ) or just the quantification (in bold) with the Bio-SmallChip ( b , d , f ).
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Images

1) Product Images from "Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs"

Article Title: Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs

Journal: Scientific Reports

doi: 10.1038/s41598-017-08134-3

Electropherograms obtained with the Bioanalyzer 2100 in miRNA-Ref and plasma samples. Examples of the profiles obtained from a miRNA-Ref sample at 10 ng/μL ( a , Bio-PicoChip; ( b ), Bio-SmallChip), a miRNA-Ref sample at 1 ng/μL ( c , Bio-PicoChip; ( d ), Bio-SmallChip), and a plasma sample ( e , Bio-PicoChip; ( f ), Bio-SmallChip). The 10 ng/µL miRNA-Ref sample ( a ) was diluted to fit the detection range of the Bio-PicoChip (0.05–5 ng/µL) and the final concentration was calculated by applying the dilution factor to the value obtained by the Bioanalyzer. In the miRNA-Ref samples ( a – d ), the overall profile is consistent with the presence of ribosomic RNA enriched with small RNAs, whereas in plasma samples ( e , f ) only small RNAs, but no long RNAs, are present. All electropherograms include the corresponding quantification (in bold) and the RNA integrity number (RIN) number (in italics) obtained with the Bio-PicoChip ( a , c , e ) or just the quantification (in bold) with the Bio-SmallChip ( b , d , f ).
Figure Legend Snippet: Electropherograms obtained with the Bioanalyzer 2100 in miRNA-Ref and plasma samples. Examples of the profiles obtained from a miRNA-Ref sample at 10 ng/μL ( a , Bio-PicoChip; ( b ), Bio-SmallChip), a miRNA-Ref sample at 1 ng/μL ( c , Bio-PicoChip; ( d ), Bio-SmallChip), and a plasma sample ( e , Bio-PicoChip; ( f ), Bio-SmallChip). The 10 ng/µL miRNA-Ref sample ( a ) was diluted to fit the detection range of the Bio-PicoChip (0.05–5 ng/µL) and the final concentration was calculated by applying the dilution factor to the value obtained by the Bioanalyzer. In the miRNA-Ref samples ( a – d ), the overall profile is consistent with the presence of ribosomic RNA enriched with small RNAs, whereas in plasma samples ( e , f ) only small RNAs, but no long RNAs, are present. All electropherograms include the corresponding quantification (in bold) and the RNA integrity number (RIN) number (in italics) obtained with the Bio-PicoChip ( a , c , e ) or just the quantification (in bold) with the Bio-SmallChip ( b , d , f ).

Techniques Used: Concentration Assay

2) Product Images from "Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy"

Article Title: Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy

Journal: Scientific Reports

doi: 10.1038/s41598-019-39111-7

Detailed workflow of the cell lysis optimization to obtain both high-quality gDNA and mRNA from the same TE biopsy. TE-A is the “clinically representative” control biopsy, lysed and processed using the standard clinical workflow for PGT-A. TE-B is the test biopsy, where cells are lysed with either SMART (Method 1) or SurePlex® (Method 2) kits. The lysate was split and processed according to the standard SurePlex® protocol for gDNA amplification, or the standard SMART-seq® protocol for cDNA synthesis. Lysis of biopsied cells with SurePlex® yields high-quality gDNA and mRNA. From each blastocyst cDNA was synthesized, amplified, and its integrity/quality was assessed by BioAnalyzer 2100 (Agilent Technologies, CA). All samples, regardless of lysis method, produced high-quality cDNA. However, only the sample lysed using SurePlex® (Method 2) produced both high-quality cDNA and gDNA which passed all clinical quality control metrics after NGS using VeriSeq® kit (highlighted with blue arrows).
Figure Legend Snippet: Detailed workflow of the cell lysis optimization to obtain both high-quality gDNA and mRNA from the same TE biopsy. TE-A is the “clinically representative” control biopsy, lysed and processed using the standard clinical workflow for PGT-A. TE-B is the test biopsy, where cells are lysed with either SMART (Method 1) or SurePlex® (Method 2) kits. The lysate was split and processed according to the standard SurePlex® protocol for gDNA amplification, or the standard SMART-seq® protocol for cDNA synthesis. Lysis of biopsied cells with SurePlex® yields high-quality gDNA and mRNA. From each blastocyst cDNA was synthesized, amplified, and its integrity/quality was assessed by BioAnalyzer 2100 (Agilent Technologies, CA). All samples, regardless of lysis method, produced high-quality cDNA. However, only the sample lysed using SurePlex® (Method 2) produced both high-quality cDNA and gDNA which passed all clinical quality control metrics after NGS using VeriSeq® kit (highlighted with blue arrows).

Techniques Used: Lysis, Amplification, Synthesized, Produced, Next-Generation Sequencing

3) Product Images from "RNase L Induces Autophagy via c-Jun N-terminal Kinase and Double-stranded RNA-dependent Protein Kinase Signaling Pathways *"

Article Title: RNase L Induces Autophagy via c-Jun N-terminal Kinase and Double-stranded RNA-dependent Protein Kinase Signaling Pathways *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M112.399964

2–5A-mediated activation of RNase L induces autophagy. A , HT1080 cells were transfected with 10 μ m  of 2–5A and cleavage of rRNA (shown by  arrows ) was analyzed on RNA chips using Agilent Bioanalyzer 2100.  B , 2–5A was transfected
Figure Legend Snippet: 2–5A-mediated activation of RNase L induces autophagy. A , HT1080 cells were transfected with 10 μ m of 2–5A and cleavage of rRNA (shown by arrows ) was analyzed on RNA chips using Agilent Bioanalyzer 2100. B , 2–5A was transfected

Techniques Used: Activation Assay, Transfection

4) Product Images from "RNase L Cleavage Products Promote Switch from Autophagy to Apoptosis by Caspase-Mediated Cleavage of Beclin-1"

Article Title: RNase L Cleavage Products Promote Switch from Autophagy to Apoptosis by Caspase-Mediated Cleavage of Beclin-1

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms160817611

Cleavage of Beclin-1 in RNase L-mediated cross-talk between autophagy and apoptosis. HT1080 cells were transfected with 10 µM of 2–5A or 2 µg/mL of PolyI:C and ( A ) RNase L-mediated cleavage of rRNA (arrows) was analyzed on RNA chips using the Agilent Bioanalyzer 2100 after 6 h. Cell viability was determined at indicated times by ( B ) MTT colorimetric assays, ( C ) trypan blue dye exclusion assay normalized to control cells or ( D ) uptake of PI by dying cells as measured by flow cytometry after staining with PI. Results are representative of three independent experiments performed in triplicate ± SD; ( E ) Cleavage of Caspase 3 and PARP in cell lysates from 2–5A or PolyI:C transfected cells was analyzed on immunoblots and normalized to β-actin levels; ( F ) Caspase 3/7 activity was measured in 2–5A transfected cells at indicated times using rhodamine-labeled caspase-3 and -7 substrate (ApoONE homogenous caspase-3 and -7 assay kit (Promega). Results are representative of three independent experiments performed in triplicate ± SD; ( G ) GFP-LC3 expressing HT1080 cells were mock treated, transfected with 10 µM of 2–5A or 2 µg/mL of PolyI:C for indicated times and the percentage of GFP + cells showing puncta formation compared to mock treated cells was analyzed. Results shown represent mean ± SEM for three experiments and at least 100 cells were analyzed per assay, p values are shown as compared with mock treated cells; ( H ) Cleavage of Beclin-1 was monitored in response to 2–5A or PolyI:C for indicated times on immunoblots and normalized to β-actin levels; ( I ) HT1080 cells expressing Flag-Beclin-1 were pretreated with zVAD-FMK (20 µM) or not for 1 h followed by 2 µg/mL of PolyI:C for indicated times. Cleavage of Beclin-1 was determined on immunoblots and normalized to β-actin levels. Results are representative of three independent experiments. Student’s t test was used to determine p values. * p
Figure Legend Snippet: Cleavage of Beclin-1 in RNase L-mediated cross-talk between autophagy and apoptosis. HT1080 cells were transfected with 10 µM of 2–5A or 2 µg/mL of PolyI:C and ( A ) RNase L-mediated cleavage of rRNA (arrows) was analyzed on RNA chips using the Agilent Bioanalyzer 2100 after 6 h. Cell viability was determined at indicated times by ( B ) MTT colorimetric assays, ( C ) trypan blue dye exclusion assay normalized to control cells or ( D ) uptake of PI by dying cells as measured by flow cytometry after staining with PI. Results are representative of three independent experiments performed in triplicate ± SD; ( E ) Cleavage of Caspase 3 and PARP in cell lysates from 2–5A or PolyI:C transfected cells was analyzed on immunoblots and normalized to β-actin levels; ( F ) Caspase 3/7 activity was measured in 2–5A transfected cells at indicated times using rhodamine-labeled caspase-3 and -7 substrate (ApoONE homogenous caspase-3 and -7 assay kit (Promega). Results are representative of three independent experiments performed in triplicate ± SD; ( G ) GFP-LC3 expressing HT1080 cells were mock treated, transfected with 10 µM of 2–5A or 2 µg/mL of PolyI:C for indicated times and the percentage of GFP + cells showing puncta formation compared to mock treated cells was analyzed. Results shown represent mean ± SEM for three experiments and at least 100 cells were analyzed per assay, p values are shown as compared with mock treated cells; ( H ) Cleavage of Beclin-1 was monitored in response to 2–5A or PolyI:C for indicated times on immunoblots and normalized to β-actin levels; ( I ) HT1080 cells expressing Flag-Beclin-1 were pretreated with zVAD-FMK (20 µM) or not for 1 h followed by 2 µg/mL of PolyI:C for indicated times. Cleavage of Beclin-1 was determined on immunoblots and normalized to β-actin levels. Results are representative of three independent experiments. Student’s t test was used to determine p values. * p

Techniques Used: Transfection, MTT Assay, Exclusion Assay, Flow Cytometry, Cytometry, Staining, Western Blot, Activity Assay, Labeling, Expressing

5) Product Images from "Gene Expression Analysis of In Vivo Fluorescent Cells"

Article Title: Gene Expression Analysis of In Vivo Fluorescent Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0001151

RNA analysis by the Bioanalyzer 2100. ( A ) RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method described here. ( B ) RNA isolated from frozen tissue by the optimized proteinase K/acid phenol method. ( C ) RNA isolated from fixed tissue by TRIzol method. ( D ) RNA isolated from fixed tissue by RNeasy Micro Kit.  (E)  One round of amplification of RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method. ( F ) One round of amplification of Ambion Control RNA. ( G ) Two rounds of amplification of RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method. ( H ) RNA ladder: first peak is RNA marker, next mark 200, 500, 1000, 2000, 4000 and 6000 nt.
Figure Legend Snippet: RNA analysis by the Bioanalyzer 2100. ( A ) RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method described here. ( B ) RNA isolated from frozen tissue by the optimized proteinase K/acid phenol method. ( C ) RNA isolated from fixed tissue by TRIzol method. ( D ) RNA isolated from fixed tissue by RNeasy Micro Kit. (E) One round of amplification of RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method. ( F ) One round of amplification of Ambion Control RNA. ( G ) Two rounds of amplification of RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method. ( H ) RNA ladder: first peak is RNA marker, next mark 200, 500, 1000, 2000, 4000 and 6000 nt.

Techniques Used: Isolation, Amplification, Marker

6) Product Images from "RNase L amplifies Interferon signaling by inducing PKR-mediated antiviral stress granules"

Article Title: RNase L amplifies Interferon signaling by inducing PKR-mediated antiviral stress granules

Journal: bioRxiv

doi: 10.1101/2020.02.07.939645

Activation of RNase L induces antiviral stress granules formation. HT1080 cells were transfected with 2–5A (10 µM) for 8h and (A) RNase L-mediated cleavage of rRNA (arrows) was analyzed on RNA chips using the Agilent Bioanalyzer 2100, RNA Integrity Number (RIN) is shown, (B) cells were fixed and stained with G3BP1 and indicated antiviral proteins, the magnified images correspond to the boxed regions, (right) intensity profiles of G3BP1 and antiviral proteins along the plotted lines as analyzed by Image J line scan analysis and (C) the percentage of cells forming stress granules were quantitated. (D) RNase L KO cells were either mock transfected or transfected with FLAG-WT-RNase L or FLAG-R667A-RNase L and immunostained for G3BP1 and FLAG, (right) intensity profiles of G3BP1 and FLAG along the plotted lines as analyzed by Image J line scan analysis. HT1080 cells were treated with H 2 O 2  (1 mM) for 3h and (E) the percentage of cells forming stress granules were quantitated, (F) cells were immunostained with G3BP1 and indicated antiviral proteins (right) intensity profiles of G3BP1 and antiviral proteins along the plotted lines as analyzed by Image J line scan analysis. All experiments included at least 100 cells from three replicates. Scale bars correspond to 10µm. Data are representative of at least three independent experiments. *p
Figure Legend Snippet: Activation of RNase L induces antiviral stress granules formation. HT1080 cells were transfected with 2–5A (10 µM) for 8h and (A) RNase L-mediated cleavage of rRNA (arrows) was analyzed on RNA chips using the Agilent Bioanalyzer 2100, RNA Integrity Number (RIN) is shown, (B) cells were fixed and stained with G3BP1 and indicated antiviral proteins, the magnified images correspond to the boxed regions, (right) intensity profiles of G3BP1 and antiviral proteins along the plotted lines as analyzed by Image J line scan analysis and (C) the percentage of cells forming stress granules were quantitated. (D) RNase L KO cells were either mock transfected or transfected with FLAG-WT-RNase L or FLAG-R667A-RNase L and immunostained for G3BP1 and FLAG, (right) intensity profiles of G3BP1 and FLAG along the plotted lines as analyzed by Image J line scan analysis. HT1080 cells were treated with H 2 O 2 (1 mM) for 3h and (E) the percentage of cells forming stress granules were quantitated, (F) cells were immunostained with G3BP1 and indicated antiviral proteins (right) intensity profiles of G3BP1 and antiviral proteins along the plotted lines as analyzed by Image J line scan analysis. All experiments included at least 100 cells from three replicates. Scale bars correspond to 10µm. Data are representative of at least three independent experiments. *p

Techniques Used: Activation Assay, Transfection, Staining

7) Product Images from "Gene Expression Analysis of In Vivo Fluorescent Cells"

Article Title: Gene Expression Analysis of In Vivo Fluorescent Cells

Journal: PLoS ONE

doi: 10.1371/journal.pone.0001151

RNA analysis by the Bioanalyzer 2100. ( A ) RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method described here. ( B ) RNA isolated from frozen tissue by the optimized proteinase K/acid phenol method. ( C ) RNA isolated from fixed tissue by TRIzol method. ( D ) RNA isolated from fixed tissue by RNeasy Micro Kit.  (E)  One round of amplification of RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method. ( F ) One round of amplification of Ambion Control RNA. ( G ) Two rounds of amplification of RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method. ( H ) RNA ladder: first peak is RNA marker, next mark 200, 500, 1000, 2000, 4000 and 6000 nt.
Figure Legend Snippet: RNA analysis by the Bioanalyzer 2100. ( A ) RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method described here. ( B ) RNA isolated from frozen tissue by the optimized proteinase K/acid phenol method. ( C ) RNA isolated from fixed tissue by TRIzol method. ( D ) RNA isolated from fixed tissue by RNeasy Micro Kit. (E) One round of amplification of RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method. ( F ) One round of amplification of Ambion Control RNA. ( G ) Two rounds of amplification of RNA isolated from fixed tissue by the optimized proteinase K/acid phenol method. ( H ) RNA ladder: first peak is RNA marker, next mark 200, 500, 1000, 2000, 4000 and 6000 nt.

Techniques Used: Isolation, Amplification, Marker

8) Product Images from "Genome-wide profiling of the 3' ends of polyadenylated RNAs"

Article Title: Genome-wide profiling of the 3' ends of polyadenylated RNAs

Journal: Methods (San Diego, Calif.)

doi: 10.1016/j.ymeth.2017.06.003

Example Agilent Bioanalyzer 2100 trace of 3'-seq library. High quality library should result in a size range distribution as expected from the size range extracted from the gel. Shown is a 3'-seq library that falls in the 150–250 bp size range (labeled). Isolation of a fraction of reads below 175bp is to be expected and will still results in reads that can be mapped to the genome. The peak should be above 130 bp to avoid contamination of adapter-adapter reads (~120 bp). On the right side the densitometry plot with the standard and the sample are shown. On the left an electropherogram of the sample is plotted with fluorescent intensity (FU) on the red y axis and size (nt) on the×axis. The markers run together with the sample are labeled. STD- standard.
Figure Legend Snippet: Example Agilent Bioanalyzer 2100 trace of 3'-seq library. High quality library should result in a size range distribution as expected from the size range extracted from the gel. Shown is a 3'-seq library that falls in the 150–250 bp size range (labeled). Isolation of a fraction of reads below 175bp is to be expected and will still results in reads that can be mapped to the genome. The peak should be above 130 bp to avoid contamination of adapter-adapter reads (~120 bp). On the right side the densitometry plot with the standard and the sample are shown. On the left an electropherogram of the sample is plotted with fluorescent intensity (FU) on the red y axis and size (nt) on the×axis. The markers run together with the sample are labeled. STD- standard.

Techniques Used: Labeling, Isolation

Example of high quality total RNA. Total RNA quality is assessed on the basis of the quality of the predominant signal from rRNA (as labeled). The trace is from high quality total RNA from  Drosophila melanogaster  run on an Agilent Bioanalyzer 2100. Notice that insect 28S rRNA dissociates into two subunits of equal size that co- migrate with the 18S rRNA. The migration of rRNA of other organisms will vary and should be taken into account when validating total RNA quality. Bioanalyzer output is shown. On the right the densitometry plot with the standard and the sample are shown. On the left an electropherogram of the sample is plotted with fluorescent intensity (FU) on the red y axis and size (nt) on the×axis. The marker run together with the sample is labeled. STD- standard.
Figure Legend Snippet: Example of high quality total RNA. Total RNA quality is assessed on the basis of the quality of the predominant signal from rRNA (as labeled). The trace is from high quality total RNA from Drosophila melanogaster run on an Agilent Bioanalyzer 2100. Notice that insect 28S rRNA dissociates into two subunits of equal size that co- migrate with the 18S rRNA. The migration of rRNA of other organisms will vary and should be taken into account when validating total RNA quality. Bioanalyzer output is shown. On the right the densitometry plot with the standard and the sample are shown. On the left an electropherogram of the sample is plotted with fluorescent intensity (FU) on the red y axis and size (nt) on the×axis. The marker run together with the sample is labeled. STD- standard.

Techniques Used: Labeling, Migration, Marker

Optimization of fragmentation time. Agilent Bioanalyzer 2100 traces of the reaction outlined in 2.2.3 stopped at different time intervals. The chemical fragmentation reaction should be stopped when the total RNA peak is around 150–200 nt (10 min) but before the RNA is completely fragmented as shown in the later time points. This step was optimized for fragmentation of Drosophila total RNA and should be optimized when using this protocol to determine 3' ends from total RNA of other organisms. Densitometry of the samples run is shown to the left while electropherograms are shown on the right. Samples are labeled above each lane and on each corresponding inset on the right. The marker, present in each sample, is labeled in the top most panel. STD- standard. FU - fluorescent intensity.
Figure Legend Snippet: Optimization of fragmentation time. Agilent Bioanalyzer 2100 traces of the reaction outlined in 2.2.3 stopped at different time intervals. The chemical fragmentation reaction should be stopped when the total RNA peak is around 150–200 nt (10 min) but before the RNA is completely fragmented as shown in the later time points. This step was optimized for fragmentation of Drosophila total RNA and should be optimized when using this protocol to determine 3' ends from total RNA of other organisms. Densitometry of the samples run is shown to the left while electropherograms are shown on the right. Samples are labeled above each lane and on each corresponding inset on the right. The marker, present in each sample, is labeled in the top most panel. STD- standard. FU - fluorescent intensity.

Techniques Used: Labeling, Marker

9) Product Images from "How do megakaryocytic microparticles target and deliver cargo to alter the fate of hematopoietic stem cells?"

Article Title: How do megakaryocytic microparticles target and deliver cargo to alter the fate of hematopoietic stem cells?

Journal: Journal of controlled release : official journal of the Controlled Release Society

doi: 10.1016/j.jconrel.2016.12.021

RNA profile of Mk and MkMP with or without RNase treatment (A) MkMPs were first treated with or without RNase I for 2 hours at 37 °C. After incubated with RNase inhibitors and washed with IMDM thrice, total RNA were isolated from MkMPs and RNA profiles were analyzed by Bioanalyzer 2100. (B) RNA profile of d12 Mks. (A) presents the data from two biological replicates to demonstrate the exquisite reproducibility of the RNA profiles before and after RNase treatment. The symbol (#) in (A) and (B) marks the range of small RNAs. 18S and 28S represent rRNA, while (δ) in (A) and (B) marks the ladder of 25 nt. (C) RNA profile of ladders for size verification. (D) Total RNA concentration from MkMPs treated with or without were measured by Qubit RNA HS kit. The measurement shows 65.5% of RNA being digested after RNA treatment. The data represent two biological replicates ± standard deviation.
Figure Legend Snippet: RNA profile of Mk and MkMP with or without RNase treatment (A) MkMPs were first treated with or without RNase I for 2 hours at 37 °C. After incubated with RNase inhibitors and washed with IMDM thrice, total RNA were isolated from MkMPs and RNA profiles were analyzed by Bioanalyzer 2100. (B) RNA profile of d12 Mks. (A) presents the data from two biological replicates to demonstrate the exquisite reproducibility of the RNA profiles before and after RNase treatment. The symbol (#) in (A) and (B) marks the range of small RNAs. 18S and 28S represent rRNA, while (δ) in (A) and (B) marks the ladder of 25 nt. (C) RNA profile of ladders for size verification. (D) Total RNA concentration from MkMPs treated with or without were measured by Qubit RNA HS kit. The measurement shows 65.5% of RNA being digested after RNA treatment. The data represent two biological replicates ± standard deviation.

Techniques Used: Incubation, Isolation, Concentration Assay, Standard Deviation

10) Product Images from "Hemoprotein Bach1 regulates enhancer availability of heme oxygenase-1 gene"

Article Title: Hemoprotein Bach1 regulates enhancer availability of heme oxygenase-1 gene

Journal: The EMBO Journal

doi: 10.1093/emboj/cdf516

Fig. 6.  Binding of small Maf to  ho-1  enhancers  in vivo . ( A ) Gel images showing PCR amplification of E2, exon 1 and Rag-2 gene fragments recovered in the absence or presence of anti-small Maf antibodies. Chromatin was prepared from the wild-type (WT) or  bach1 -deficient (KO) thymi. PCR products without DNA template are shown in the right-hand lanes. ( B ) Fold-enrichment of each genomic DNA region by the small Maf antibodies was determined using the Agilent BioAnalyzer 2100. Results are mean of two experiments using two mice per each genotype. ( C ) A hypothetical model describing the regulation of  ho-1  by Bach1 and heme. Besides MafK, other Maf-related factors may also serve as partners for Bach1. Bach1 makes enhancers inaccessible to Nrf2 and other activators by binding to them. Repression by Bach1 is alleviated upon increase of heme levels, allowing expression of HO-1 followed by degradation of heme.
Figure Legend Snippet: Fig. 6. Binding of small Maf to ho-1 enhancers in vivo . ( A ) Gel images showing PCR amplification of E2, exon 1 and Rag-2 gene fragments recovered in the absence or presence of anti-small Maf antibodies. Chromatin was prepared from the wild-type (WT) or bach1 -deficient (KO) thymi. PCR products without DNA template are shown in the right-hand lanes. ( B ) Fold-enrichment of each genomic DNA region by the small Maf antibodies was determined using the Agilent BioAnalyzer 2100. Results are mean of two experiments using two mice per each genotype. ( C ) A hypothetical model describing the regulation of ho-1 by Bach1 and heme. Besides MafK, other Maf-related factors may also serve as partners for Bach1. Bach1 makes enhancers inaccessible to Nrf2 and other activators by binding to them. Repression by Bach1 is alleviated upon increase of heme levels, allowing expression of HO-1 followed by degradation of heme.

Techniques Used: Binding Assay, In Vivo, Polymerase Chain Reaction, Amplification, Mouse Assay, Expressing

Fig. 4.  Expression of HO-1 in  bach1 -deficient mice. ( A ) Protein extracts of indicated tissues of  bach1 +/+  or  bach1 –/–  (shown by W and K, respectively) mice were analyzed for expression of HO-1 by immunoblot assays (upper panels). HO-1 is indicated by an arrowhead. Membranes were stained for protein with amido black to verify equal loading (lower panels). ( B ) HO-1 and HPRT mRNA levels in thymus, heart, lung and liver from various genotypes (indicated above the panels) were compared by RT–PCR. To ensure linearity of amplification, 3-fold dilutions of cDNA (lanes 1–3 and 4–6, and indicated with H and L at the top) were used as templates. Images were recorded using the Agilent BioAnalyzer 2100.
Figure Legend Snippet: Fig. 4. Expression of HO-1 in bach1 -deficient mice. ( A ) Protein extracts of indicated tissues of bach1 +/+ or bach1 –/– (shown by W and K, respectively) mice were analyzed for expression of HO-1 by immunoblot assays (upper panels). HO-1 is indicated by an arrowhead. Membranes were stained for protein with amido black to verify equal loading (lower panels). ( B ) HO-1 and HPRT mRNA levels in thymus, heart, lung and liver from various genotypes (indicated above the panels) were compared by RT–PCR. To ensure linearity of amplification, 3-fold dilutions of cDNA (lanes 1–3 and 4–6, and indicated with H and L at the top) were used as templates. Images were recorded using the Agilent BioAnalyzer 2100.

Techniques Used: Expressing, Mouse Assay, Staining, Reverse Transcription Polymerase Chain Reaction, Amplification

11) Product Images from "Proliferation Cycle Causes Age Dependent Mitochondrial Deficiencies and Contributes to the Aging of Stem Cells"

Article Title: Proliferation Cycle Causes Age Dependent Mitochondrial Deficiencies and Contributes to the Aging of Stem Cells

Journal: Genes

doi: 10.3390/genes8120397

Mitochondrial DNA (mtDNA) rearrangements and impaired mtDNA replication in ovaries of aged flies. ( A ) Schematic drawing of  Drosophila melanogaster  (Dm.) mtDNA. Enzyme sites of HindIII (H) and XhoI (X) are indicated. Sizes of digested fragments are also labelled. ( B ) Representative gel image of rolling cycle amplification of mtDNA (arrowhead) and DNA marker (M, kb). ( C ) Pattern of rolling cycle amplification (RCA) amplified mtDNA digested by XhoI and HindIII. The 5.8 kb fragment spanning the AT-rich region was recovered for restriction fragment length polymorphism (RFLP) analysis. ( D ) Schematic map of SspI site on 5.8 kb AT-rich region. ( E ) densitometry plot of SspI digestion pattern of 5.8 fragments spanning the AT-rich region from young (2-day-old) and old (60-day-old) ovaries, analyzed by Agilent Bioanalyzer 2100. Note the difference of bands (open arrowheads) demonstrating the rearrangements of AT-rich regions in aged ovaries. DNA dye standard (closed arrowheads) and DNA ladder are marked (M, bp). ( F ) Representative images showing 5-ethynyl-2’-deoxyuridine (EdU) incorporation into mtDNA (green puncta, arrowheads) in ovaries (dashed line, anterior toward left) from young (2-day-old) and old (40-day-old) female flies. Note that the number of EdU puncta was dramatically reduced in germarium from old fly. Arrowhead: mtDNA; arrow: nuclear DNA; scale bar: 10 µm.
Figure Legend Snippet: Mitochondrial DNA (mtDNA) rearrangements and impaired mtDNA replication in ovaries of aged flies. ( A ) Schematic drawing of Drosophila melanogaster (Dm.) mtDNA. Enzyme sites of HindIII (H) and XhoI (X) are indicated. Sizes of digested fragments are also labelled. ( B ) Representative gel image of rolling cycle amplification of mtDNA (arrowhead) and DNA marker (M, kb). ( C ) Pattern of rolling cycle amplification (RCA) amplified mtDNA digested by XhoI and HindIII. The 5.8 kb fragment spanning the AT-rich region was recovered for restriction fragment length polymorphism (RFLP) analysis. ( D ) Schematic map of SspI site on 5.8 kb AT-rich region. ( E ) densitometry plot of SspI digestion pattern of 5.8 fragments spanning the AT-rich region from young (2-day-old) and old (60-day-old) ovaries, analyzed by Agilent Bioanalyzer 2100. Note the difference of bands (open arrowheads) demonstrating the rearrangements of AT-rich regions in aged ovaries. DNA dye standard (closed arrowheads) and DNA ladder are marked (M, bp). ( F ) Representative images showing 5-ethynyl-2’-deoxyuridine (EdU) incorporation into mtDNA (green puncta, arrowheads) in ovaries (dashed line, anterior toward left) from young (2-day-old) and old (40-day-old) female flies. Note that the number of EdU puncta was dramatically reduced in germarium from old fly. Arrowhead: mtDNA; arrow: nuclear DNA; scale bar: 10 µm.

Techniques Used: Amplification, Marker

12) Product Images from "Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy"

Article Title: Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy

Journal: Scientific Reports

doi: 10.1038/s41598-019-39111-7

Detailed workflow of the cell lysis optimization to obtain both high-quality gDNA and mRNA from the same TE biopsy. TE-A is the “clinically representative” control biopsy, lysed and processed using the standard clinical workflow for PGT-A. TE-B is the test biopsy, where cells are lysed with either SMART (Method 1) or SurePlex® (Method 2) kits. The lysate was split and processed according to the standard SurePlex® protocol for gDNA amplification, or the standard SMART-seq® protocol for cDNA synthesis. Lysis of biopsied cells with SurePlex® yields high-quality gDNA and mRNA. From each blastocyst cDNA was synthesized, amplified, and its integrity/quality was assessed by BioAnalyzer 2100 (Agilent Technologies, CA). All samples, regardless of lysis method, produced high-quality cDNA. However, only the sample lysed using SurePlex® (Method 2) produced both high-quality cDNA and gDNA which passed all clinical quality control metrics after NGS using VeriSeq® kit (highlighted with blue arrows).
Figure Legend Snippet: Detailed workflow of the cell lysis optimization to obtain both high-quality gDNA and mRNA from the same TE biopsy. TE-A is the “clinically representative” control biopsy, lysed and processed using the standard clinical workflow for PGT-A. TE-B is the test biopsy, where cells are lysed with either SMART (Method 1) or SurePlex® (Method 2) kits. The lysate was split and processed according to the standard SurePlex® protocol for gDNA amplification, or the standard SMART-seq® protocol for cDNA synthesis. Lysis of biopsied cells with SurePlex® yields high-quality gDNA and mRNA. From each blastocyst cDNA was synthesized, amplified, and its integrity/quality was assessed by BioAnalyzer 2100 (Agilent Technologies, CA). All samples, regardless of lysis method, produced high-quality cDNA. However, only the sample lysed using SurePlex® (Method 2) produced both high-quality cDNA and gDNA which passed all clinical quality control metrics after NGS using VeriSeq® kit (highlighted with blue arrows).

Techniques Used: Lysis, Amplification, Synthesized, Produced, Next-Generation Sequencing

13) Product Images from "Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy"

Article Title: Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy

Journal: Scientific Reports

doi: 10.1038/s41598-019-39111-7

Detailed workflow of the cell lysis optimization to obtain both high-quality gDNA and mRNA from the same TE biopsy. TE-A is the “clinically representative” control biopsy, lysed and processed using the standard clinical workflow for PGT-A. TE-B is the test biopsy, where cells are lysed with either SMART (Method 1) or SurePlex® (Method 2) kits. The lysate was split and processed according to the standard SurePlex® protocol for gDNA amplification, or the standard SMART-seq® protocol for cDNA synthesis. Lysis of biopsied cells with SurePlex® yields high-quality gDNA and mRNA. From each blastocyst cDNA was synthesized, amplified, and its integrity/quality was assessed by BioAnalyzer 2100 (Agilent Technologies, CA). All samples, regardless of lysis method, produced high-quality cDNA. However, only the sample lysed using SurePlex® (Method 2) produced both high-quality cDNA and gDNA which passed all clinical quality control metrics after NGS using VeriSeq® kit (highlighted with blue arrows).
Figure Legend Snippet: Detailed workflow of the cell lysis optimization to obtain both high-quality gDNA and mRNA from the same TE biopsy. TE-A is the “clinically representative” control biopsy, lysed and processed using the standard clinical workflow for PGT-A. TE-B is the test biopsy, where cells are lysed with either SMART (Method 1) or SurePlex® (Method 2) kits. The lysate was split and processed according to the standard SurePlex® protocol for gDNA amplification, or the standard SMART-seq® protocol for cDNA synthesis. Lysis of biopsied cells with SurePlex® yields high-quality gDNA and mRNA. From each blastocyst cDNA was synthesized, amplified, and its integrity/quality was assessed by BioAnalyzer 2100 (Agilent Technologies, CA). All samples, regardless of lysis method, produced high-quality cDNA. However, only the sample lysed using SurePlex® (Method 2) produced both high-quality cDNA and gDNA which passed all clinical quality control metrics after NGS using VeriSeq® kit (highlighted with blue arrows).

Techniques Used: Lysis, Amplification, Synthesized, Produced, Next-Generation Sequencing

14) Product Images from "AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay"

Article Title: AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay

Journal: Methods (San Diego, Calif.)

doi: 10.1016/j.ymeth.2010.04.003

Sonicated DNA. An electropherogram produced using an Agilent Bioanalyzer 2100 illustrating the size-range of DNA used in AutoMeDIP-seq. Approximately, 45% of the sample is contained between 150 and 250 bp.
Figure Legend Snippet: Sonicated DNA. An electropherogram produced using an Agilent Bioanalyzer 2100 illustrating the size-range of DNA used in AutoMeDIP-seq. Approximately, 45% of the sample is contained between 150 and 250 bp.

Techniques Used: Sonication, Produced

15) Product Images from "Preservation of Multiple Mammalian Tissues to Maximize Science Return from Ground Based and Spaceflight Experiments"

Article Title: Preservation of Multiple Mammalian Tissues to Maximize Science Return from Ground Based and Spaceflight Experiments

Journal: PLoS ONE

doi: 10.1371/journal.pone.0167391

Effects of preservation times post-euthanasia on RNA quality in spleen and liver. Spleens and livers were collected from up to 3 minutes (Positive Control), 9 minutes (Set 1), and 25 minutes (Set 2) post-euthanasia. Set 1 and 2 time points were selected to simulate anticipated dissection timing in microgravity. Spleens were preserved in RNAlater, and livers were frozen on dry ice. All samples were stored at -80°C, and analyzed after 3.5 months for spleen and 4.5 months for liver. RNA quality was measured by calculating the Bioanalyzer-based RNA integrity number (RIN) using the Bioanalyzer 2100. Samples harvested up to 25 minutes post-euthanasia, and stored for less than 5 months at -80°C, yielded RIN values greater than 8. Data sets were assessed for normality using the Shapiro-Wilk test, followed by the Kruskal-Wallis test. Values shown are medians within interquartile (boxes) and full range (whiskers). Spleens: n = 4, 9, and 8 for Control, Set 1 and 2, respectively. Livers: n = 3, 10, and 10 for Control, Set 1 and 2, respectively.
Figure Legend Snippet: Effects of preservation times post-euthanasia on RNA quality in spleen and liver. Spleens and livers were collected from up to 3 minutes (Positive Control), 9 minutes (Set 1), and 25 minutes (Set 2) post-euthanasia. Set 1 and 2 time points were selected to simulate anticipated dissection timing in microgravity. Spleens were preserved in RNAlater, and livers were frozen on dry ice. All samples were stored at -80°C, and analyzed after 3.5 months for spleen and 4.5 months for liver. RNA quality was measured by calculating the Bioanalyzer-based RNA integrity number (RIN) using the Bioanalyzer 2100. Samples harvested up to 25 minutes post-euthanasia, and stored for less than 5 months at -80°C, yielded RIN values greater than 8. Data sets were assessed for normality using the Shapiro-Wilk test, followed by the Kruskal-Wallis test. Values shown are medians within interquartile (boxes) and full range (whiskers). Spleens: n = 4, 9, and 8 for Control, Set 1 and 2, respectively. Livers: n = 3, 10, and 10 for Control, Set 1 and 2, respectively.

Techniques Used: Preserving, Positive Control, Dissection

16) Product Images from "Time-Dependent Decay of mRNA and Ribosomal RNA during Platelet Aging and Its Correlation with Translation Activity"

Article Title: Time-Dependent Decay of mRNA and Ribosomal RNA during Platelet Aging and Its Correlation with Translation Activity

Journal: PLoS ONE

doi: 10.1371/journal.pone.0148064

Fate of human PLT RNAs in transfusion bags. Transfusion bags were incubated and sampled at 22°C or 37°C for 0, 6, 20 or 48 h. PLT activation was checked by FC after staining with FITC-conjugated annexin V or anti-P-selectin mAb. Total RNA was extracted and analyzed on a Bioanalyzer 2100 and electropherograms of the extracted RNA are shown. The 28S/18S RNA ratios are indicated between the rRNA peaks and the percentages of small RNAs are shown above the small RNA peaks. AnnV and P-Sel, percentage of annexin V- and P-selectin-positive PLTs (ND, not determined).
Figure Legend Snippet: Fate of human PLT RNAs in transfusion bags. Transfusion bags were incubated and sampled at 22°C or 37°C for 0, 6, 20 or 48 h. PLT activation was checked by FC after staining with FITC-conjugated annexin V or anti-P-selectin mAb. Total RNA was extracted and analyzed on a Bioanalyzer 2100 and electropherograms of the extracted RNA are shown. The 28S/18S RNA ratios are indicated between the rRNA peaks and the percentages of small RNAs are shown above the small RNA peaks. AnnV and P-Sel, percentage of annexin V- and P-selectin-positive PLTs (ND, not determined).

Techniques Used: Incubation, Activation Assay, Staining

17) Product Images from "Small RNA Sequencing for Profiling MicroRNAs in Long-Term Preserved Formalin-Fixed and Paraffin-Embedded Non-Small Cell Lung Cancer Tumor Specimens"

Article Title: Small RNA Sequencing for Profiling MicroRNAs in Long-Term Preserved Formalin-Fixed and Paraffin-Embedded Non-Small Cell Lung Cancer Tumor Specimens

Journal: PLoS ONE

doi: 10.1371/journal.pone.0121521

Assessment of total RNA extracted from FFPE tissues. A. Correlation between measurements of RNA yield (μg) obtained using absorbance at 260 nm or fluorescence with RiboGreen dye (n = 8). The lines of identity and linear regression (least squares method) and values and 95% confidence intervals of the Pearson coefficient ( r ) and slope of linear regression ( m );  P -values are also noted. B. Electrophoretogram of the 8 RNA samples ( A - H ). Samples were run on an Agilent Eukaryote Total RNA Pico chip on Bioanalyzer 2100. Sizes of molecular weight markers and the RNA integrity numbers are noted.
Figure Legend Snippet: Assessment of total RNA extracted from FFPE tissues. A. Correlation between measurements of RNA yield (μg) obtained using absorbance at 260 nm or fluorescence with RiboGreen dye (n = 8). The lines of identity and linear regression (least squares method) and values and 95% confidence intervals of the Pearson coefficient ( r ) and slope of linear regression ( m ); P -values are also noted. B. Electrophoretogram of the 8 RNA samples ( A - H ). Samples were run on an Agilent Eukaryote Total RNA Pico chip on Bioanalyzer 2100. Sizes of molecular weight markers and the RNA integrity numbers are noted.

Techniques Used: Formalin-fixed Paraffin-Embedded, Fluorescence, Chromatin Immunoprecipitation, Molecular Weight

18) Product Images from "Exploiting Pre-rRNA Processing in Diamond Blackfan Anemia Gene Discovery and Diagnosis"

Article Title: Exploiting Pre-rRNA Processing in Diamond Blackfan Anemia Gene Discovery and Diagnosis

Journal: American journal of hematology

doi: 10.1002/ajh.23807

Representative Agilent Bioanalyzer 2100 electrophoretogram data demonstrates prominent peaks corresponding to 18S and 28S rRNA, with a minor peak just larger than 28S rRNA corresponding to 32S pre-RNA, that was evident in analysis of total RNA from ConA-stimulated
Figure Legend Snippet: Representative Agilent Bioanalyzer 2100 electrophoretogram data demonstrates prominent peaks corresponding to 18S and 28S rRNA, with a minor peak just larger than 28S rRNA corresponding to 32S pre-RNA, that was evident in analysis of total RNA from ConA-stimulated

Techniques Used:

19) Product Images from "Hemoprotein Bach1 regulates enhancer availability of heme oxygenase-1 gene"

Article Title: Hemoprotein Bach1 regulates enhancer availability of heme oxygenase-1 gene

Journal: The EMBO Journal

doi: 10.1093/emboj/cdf516

Fig. 6.  Binding of small Maf to  ho-1  enhancers  in vivo . ( A ) Gel images showing PCR amplification of E2, exon 1 and Rag-2 gene fragments recovered in the absence or presence of anti-small Maf antibodies. Chromatin was prepared from the wild-type (WT) or  bach1 -deficient (KO) thymi. PCR products without DNA template are shown in the right-hand lanes. ( B ) Fold-enrichment of each genomic DNA region by the small Maf antibodies was determined using the Agilent BioAnalyzer 2100. Results are mean of two experiments using two mice per each genotype. ( C ) A hypothetical model describing the regulation of  ho-1  by Bach1 and heme. Besides MafK, other Maf-related factors may also serve as partners for Bach1. Bach1 makes enhancers inaccessible to Nrf2 and other activators by binding to them. Repression by Bach1 is alleviated upon increase of heme levels, allowing expression of HO-1 followed by degradation of heme.
Figure Legend Snippet: Fig. 6. Binding of small Maf to ho-1 enhancers in vivo . ( A ) Gel images showing PCR amplification of E2, exon 1 and Rag-2 gene fragments recovered in the absence or presence of anti-small Maf antibodies. Chromatin was prepared from the wild-type (WT) or bach1 -deficient (KO) thymi. PCR products without DNA template are shown in the right-hand lanes. ( B ) Fold-enrichment of each genomic DNA region by the small Maf antibodies was determined using the Agilent BioAnalyzer 2100. Results are mean of two experiments using two mice per each genotype. ( C ) A hypothetical model describing the regulation of ho-1 by Bach1 and heme. Besides MafK, other Maf-related factors may also serve as partners for Bach1. Bach1 makes enhancers inaccessible to Nrf2 and other activators by binding to them. Repression by Bach1 is alleviated upon increase of heme levels, allowing expression of HO-1 followed by degradation of heme.

Techniques Used: Binding Assay, In Vivo, Polymerase Chain Reaction, Amplification, Mouse Assay, Expressing

Fig. 4.  Expression of HO-1 in  bach1 -deficient mice. ( A ) Protein extracts of indicated tissues of  bach1 +/+  or  bach1 –/–  (shown by W and K, respectively) mice were analyzed for expression of HO-1 by immunoblot assays (upper panels). HO-1 is indicated by an arrowhead. Membranes were stained for protein with amido black to verify equal loading (lower panels). ( B ) HO-1 and HPRT mRNA levels in thymus, heart, lung and liver from various genotypes (indicated above the panels) were compared by RT–PCR. To ensure linearity of amplification, 3-fold dilutions of cDNA (lanes 1–3 and 4–6, and indicated with H and L at the top) were used as templates. Images were recorded using the Agilent BioAnalyzer 2100.
Figure Legend Snippet: Fig. 4. Expression of HO-1 in bach1 -deficient mice. ( A ) Protein extracts of indicated tissues of bach1 +/+ or bach1 –/– (shown by W and K, respectively) mice were analyzed for expression of HO-1 by immunoblot assays (upper panels). HO-1 is indicated by an arrowhead. Membranes were stained for protein with amido black to verify equal loading (lower panels). ( B ) HO-1 and HPRT mRNA levels in thymus, heart, lung and liver from various genotypes (indicated above the panels) were compared by RT–PCR. To ensure linearity of amplification, 3-fold dilutions of cDNA (lanes 1–3 and 4–6, and indicated with H and L at the top) were used as templates. Images were recorded using the Agilent BioAnalyzer 2100.

Techniques Used: Expressing, Mouse Assay, Staining, Reverse Transcription Polymerase Chain Reaction, Amplification

20) Product Images from "A comparison of commercially-available automated and manual extraction kits for the isolation of total RNA from small tissue samples"

Article Title: A comparison of commercially-available automated and manual extraction kits for the isolation of total RNA from small tissue samples

Journal: BMC Biotechnology

doi: 10.1186/s12896-014-0094-8

A representative example of the gel images produced during RNA quality checks performed via the Bioanalyzer 2100.  The composite gel image was generated from the results of RNA quality assessments performed on RNA extracted from larvae samples. For each kit, the lane corresponding to the sample that best represented the “average” RNA yielded is included. The first number reported for each kit represents the RIN value of the sample shown, while the numbers below represent the mean RIN value (± standard deviation) for all larvae samples extracted via each kit. Note that the lanes shown in the image were not obtained from samples run on the same Nanochip resulting in the misalignment of the 18S and 28S bands between some of the lanes.
Figure Legend Snippet: A representative example of the gel images produced during RNA quality checks performed via the Bioanalyzer 2100. The composite gel image was generated from the results of RNA quality assessments performed on RNA extracted from larvae samples. For each kit, the lane corresponding to the sample that best represented the “average” RNA yielded is included. The first number reported for each kit represents the RIN value of the sample shown, while the numbers below represent the mean RIN value (± standard deviation) for all larvae samples extracted via each kit. Note that the lanes shown in the image were not obtained from samples run on the same Nanochip resulting in the misalignment of the 18S and 28S bands between some of the lanes.

Techniques Used: Produced, Generated, Standard Deviation

21) Product Images from "Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy"

Article Title: Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy

Journal: Scientific Reports

doi: 10.1038/s41598-019-39111-7

Detailed workflow of the cell lysis optimization to obtain both high-quality gDNA and mRNA from the same TE biopsy. TE-A is the “clinically representative” control biopsy, lysed and processed using the standard clinical workflow for PGT-A. TE-B is the test biopsy, where cells are lysed with either SMART (Method 1) or SurePlex® (Method 2) kits. The lysate was split and processed according to the standard SurePlex® protocol for gDNA amplification, or the standard SMART-seq® protocol for cDNA synthesis. Lysis of biopsied cells with SurePlex® yields high-quality gDNA and mRNA. From each blastocyst cDNA was synthesized, amplified, and its integrity/quality was assessed by BioAnalyzer 2100 (Agilent Technologies, CA). All samples, regardless of lysis method, produced high-quality cDNA. However, only the sample lysed using SurePlex® (Method 2) produced both high-quality cDNA and gDNA which passed all clinical quality control metrics after NGS using VeriSeq® kit (highlighted with blue arrows).
Figure Legend Snippet: Detailed workflow of the cell lysis optimization to obtain both high-quality gDNA and mRNA from the same TE biopsy. TE-A is the “clinically representative” control biopsy, lysed and processed using the standard clinical workflow for PGT-A. TE-B is the test biopsy, where cells are lysed with either SMART (Method 1) or SurePlex® (Method 2) kits. The lysate was split and processed according to the standard SurePlex® protocol for gDNA amplification, or the standard SMART-seq® protocol for cDNA synthesis. Lysis of biopsied cells with SurePlex® yields high-quality gDNA and mRNA. From each blastocyst cDNA was synthesized, amplified, and its integrity/quality was assessed by BioAnalyzer 2100 (Agilent Technologies, CA). All samples, regardless of lysis method, produced high-quality cDNA. However, only the sample lysed using SurePlex® (Method 2) produced both high-quality cDNA and gDNA which passed all clinical quality control metrics after NGS using VeriSeq® kit (highlighted with blue arrows).

Techniques Used: Lysis, Amplification, Synthesized, Produced, Next-Generation Sequencing

22) Product Images from "Gene expression dataset for whole cochlea of Macaca fascicularis"

Article Title: Gene expression dataset for whole cochlea of Macaca fascicularis

Journal: Scientific Reports

doi: 10.1038/s41598-018-33985-9

Schematic procedures to extract cochlear signature genes from  M. fascicularis . ( a ) A dissected cochlea along with the modiolus. Tissues shown within the green dotted line were dissected out as whole cochlea and subjected to RNA extraction. Scale bar = 1 cm. ( b ) Histochemical image of a  M. fascicularis  cochlea stained with hematoxylin and eosin to show that the dissected “whole cochlea” in ( a ) corresponds to the membranous tissues of the cochlea. Scale bar = 500 μm. ( c ) Evaluation of the quality of RNA extracted from the left cochlea, as assessed with a Bioanalyzer 2100. Arrowheads indicate peaks of 18S and 28S rRNA. ( d ) Procedures of the analysis. Individual gene expression data in the left and right cochleae using the (experiment 1, top) macaque or (experiment 2, bottom) human microarray were compared with averaged expression levels of three or one macaque animals in duplicate and/or pooled human tissues or cells to extract probes that had expression levels  > 2-fold compared with the average of all the tissues and  P
Figure Legend Snippet: Schematic procedures to extract cochlear signature genes from M. fascicularis . ( a ) A dissected cochlea along with the modiolus. Tissues shown within the green dotted line were dissected out as whole cochlea and subjected to RNA extraction. Scale bar = 1 cm. ( b ) Histochemical image of a M. fascicularis cochlea stained with hematoxylin and eosin to show that the dissected “whole cochlea” in ( a ) corresponds to the membranous tissues of the cochlea. Scale bar = 500 μm. ( c ) Evaluation of the quality of RNA extracted from the left cochlea, as assessed with a Bioanalyzer 2100. Arrowheads indicate peaks of 18S and 28S rRNA. ( d ) Procedures of the analysis. Individual gene expression data in the left and right cochleae using the (experiment 1, top) macaque or (experiment 2, bottom) human microarray were compared with averaged expression levels of three or one macaque animals in duplicate and/or pooled human tissues or cells to extract probes that had expression levels > 2-fold compared with the average of all the tissues and P

Techniques Used: RNA Extraction, Staining, Expressing, Microarray

23) Product Images from "Time-Dependent Decay of mRNA and Ribosomal RNA during Platelet Aging and Its Correlation with Translation Activity"

Article Title: Time-Dependent Decay of mRNA and Ribosomal RNA during Platelet Aging and Its Correlation with Translation Activity

Journal: PLoS ONE

doi: 10.1371/journal.pone.0148064

Fate of human PLT RNAs in transfusion bags. Transfusion bags were incubated and sampled at 22°C or 37°C for 0, 6, 20 or 48 h. PLT activation was checked by FC after staining with FITC-conjugated annexin V or anti-P-selectin mAb. Total RNA was extracted and analyzed on a Bioanalyzer 2100 and electropherograms of the extracted RNA are shown. The 28S/18S RNA ratios are indicated between the rRNA peaks and the percentages of small RNAs are shown above the small RNA peaks. AnnV and P-Sel, percentage of annexin V- and P-selectin-positive PLTs (ND, not determined).
Figure Legend Snippet: Fate of human PLT RNAs in transfusion bags. Transfusion bags were incubated and sampled at 22°C or 37°C for 0, 6, 20 or 48 h. PLT activation was checked by FC after staining with FITC-conjugated annexin V or anti-P-selectin mAb. Total RNA was extracted and analyzed on a Bioanalyzer 2100 and electropherograms of the extracted RNA are shown. The 28S/18S RNA ratios are indicated between the rRNA peaks and the percentages of small RNAs are shown above the small RNA peaks. AnnV and P-Sel, percentage of annexin V- and P-selectin-positive PLTs (ND, not determined).

Techniques Used: Incubation, Activation Assay, Staining

24) Product Images from "Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research"

Article Title: Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research

Journal: Scientific Reports

doi: 10.1038/s41598-019-56509-5

RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.
Figure Legend Snippet: RNA quality of cultivated tissue slices. RNA quality was determined by a Bioanalyzer 2100 using the RNA 6000 Nano-Kit (Agilent Technologies) and revealed good quality before the DNase digestion was performed ( a ). After the DNase digestion, the RNA quality was strongly reduced ( b ). The left graphs show untreated peritumoral brain tissue, the right graphs the corresponding GBM tissue.

Techniques Used:

25) Product Images from "Antibody production using a ciliate generates unusual antibody glycoforms displaying enhanced cell-killing activity"

Article Title: Antibody production using a ciliate generates unusual antibody glycoforms displaying enhanced cell-killing activity

Journal: mAbs

doi: 10.1080/19420862.2016.1228504

Expression, purification and glycoform separation of anti-CD20 antibody expressed by T. thermophila . (A) Two different expression cassettes in 2 different vectors were used to generate transgenic T. thermophila strains. The pAX_hNeoR_HC plasmid contains the full length cDNA encoding the heavy chain of anti-CD20, fused to the signal sequence of Tetrahymena PGP1 (signal peptide, amino acids 1–18), flanked by a ∼1 kb MTT1 promoter active sequence and the BTU2 terminator (∼350bp). The pKOIX_B_LC plasmid contains the full length cDNA encoding the light chain gene of anti-CD20, fused to the signal sequence of Tetrahymena PGP1 (signal peptide, amino acids 1–18), controlled by a ∼1.2 kb MTT5 promoter active sequence and the BTU2 terminator (∼350 bp). The whole expression cassette is flanked by DHFR-TS 3′ and 5′ integration sequences (each ∼1.5 kb). lx, lox promoter cassette; CmR, chloramphenicol resistance cassette, H4, Histon promotor, Ig-HC, immunoglobulin heavy chain, Ig-LC, immunoglobulin light chain, DHFR, Dihydrofolatreductase, BsdR, blasticidin resistance cassette, hNeoR, neomycin resistance cassette, BT, β tubulin terminator sequence. (B-D) Tetrahymena anti-CD20 antibody was purified from cadmium-induced cell culture supernatant using Protein A affinity chromatography. Supernatant (SN), flow-through fraction (W) and eluate fraction (E) were analyzed by SDS-PAGE and silver staining (B) and immune blot using HRP conjugated anti-human IgG antibody (C). Full IgG band of Tt /C2B8 was compared to MabThera (MT) full IgG band. Purified Tt /C2B8 and MabThera® were analyzed regarding their N-linked glycan occupancy using Bioanalyzer 2100. Antibody samples were deglycosylated by PNGaseF treatment (deglyc.) and separated under reduced (red.) and nonreduced (non red.) conditions (D). M, prestained standard. (E) Chromatogram of a representative HPLC - CEX resulting in separation of anti-CD20 antibody variants differing in heavy chain N-linked glycan occupancy. A gradient of salt at pH 4.0 was used for elution. Antibody samples from separated peaks (P1 – P3) were analyzed using Bioanalyzer 2100 (P1, 99% glycosylated HC; P2 51% glycosylated HC; P3 24% glycosylated HC, MT, MabThera®).
Figure Legend Snippet: Expression, purification and glycoform separation of anti-CD20 antibody expressed by T. thermophila . (A) Two different expression cassettes in 2 different vectors were used to generate transgenic T. thermophila strains. The pAX_hNeoR_HC plasmid contains the full length cDNA encoding the heavy chain of anti-CD20, fused to the signal sequence of Tetrahymena PGP1 (signal peptide, amino acids 1–18), flanked by a ∼1 kb MTT1 promoter active sequence and the BTU2 terminator (∼350bp). The pKOIX_B_LC plasmid contains the full length cDNA encoding the light chain gene of anti-CD20, fused to the signal sequence of Tetrahymena PGP1 (signal peptide, amino acids 1–18), controlled by a ∼1.2 kb MTT5 promoter active sequence and the BTU2 terminator (∼350 bp). The whole expression cassette is flanked by DHFR-TS 3′ and 5′ integration sequences (each ∼1.5 kb). lx, lox promoter cassette; CmR, chloramphenicol resistance cassette, H4, Histon promotor, Ig-HC, immunoglobulin heavy chain, Ig-LC, immunoglobulin light chain, DHFR, Dihydrofolatreductase, BsdR, blasticidin resistance cassette, hNeoR, neomycin resistance cassette, BT, β tubulin terminator sequence. (B-D) Tetrahymena anti-CD20 antibody was purified from cadmium-induced cell culture supernatant using Protein A affinity chromatography. Supernatant (SN), flow-through fraction (W) and eluate fraction (E) were analyzed by SDS-PAGE and silver staining (B) and immune blot using HRP conjugated anti-human IgG antibody (C). Full IgG band of Tt /C2B8 was compared to MabThera (MT) full IgG band. Purified Tt /C2B8 and MabThera® were analyzed regarding their N-linked glycan occupancy using Bioanalyzer 2100. Antibody samples were deglycosylated by PNGaseF treatment (deglyc.) and separated under reduced (red.) and nonreduced (non red.) conditions (D). M, prestained standard. (E) Chromatogram of a representative HPLC - CEX resulting in separation of anti-CD20 antibody variants differing in heavy chain N-linked glycan occupancy. A gradient of salt at pH 4.0 was used for elution. Antibody samples from separated peaks (P1 – P3) were analyzed using Bioanalyzer 2100 (P1, 99% glycosylated HC; P2 51% glycosylated HC; P3 24% glycosylated HC, MT, MabThera®).

Techniques Used: Expressing, Purification, Transgenic Assay, Plasmid Preparation, Sequencing, Cell Culture, Affinity Chromatography, Flow Cytometry, SDS Page, Silver Staining, High Performance Liquid Chromatography

26) Product Images from "Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2′-O-Methylation"

Article Title: Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2′-O-Methylation

Journal: Biomolecules

doi: 10.3390/biom7010013

Fragmentation profiles for E. coli and S. cerevisiae total tRNA fractions. Alkaline hydrolysis was performed for 6–12 min (as indicated on the traces). Fragments size was analyzed by capillary electrophoresis on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) Small RNA Chip. FU: fluorescence unit.
Figure Legend Snippet: Fragmentation profiles for E. coli and S. cerevisiae total tRNA fractions. Alkaline hydrolysis was performed for 6–12 min (as indicated on the traces). Fragments size was analyzed by capillary electrophoresis on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) Small RNA Chip. FU: fluorescence unit.

Techniques Used: Electrophoresis, Chromatin Immunoprecipitation, Fluorescence

27) Product Images from "Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2′-O-Methylation"

Article Title: Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2′-O-Methylation

Journal: Biomolecules

doi: 10.3390/biom7010013

Fragmentation profiles for E. coli and S. cerevisiae total tRNA fractions. Alkaline hydrolysis was performed for 6–12 min (as indicated on the traces). Fragments size was analyzed by capillary electrophoresis on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) Small RNA Chip. FU: fluorescence unit.
Figure Legend Snippet: Fragmentation profiles for E. coli and S. cerevisiae total tRNA fractions. Alkaline hydrolysis was performed for 6–12 min (as indicated on the traces). Fragments size was analyzed by capillary electrophoresis on a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) Small RNA Chip. FU: fluorescence unit.

Techniques Used: Electrophoresis, Chromatin Immunoprecipitation, Fluorescence

28) Product Images from "Genome-wide profiling of the 3' ends of polyadenylated RNAs"

Article Title: Genome-wide profiling of the 3' ends of polyadenylated RNAs

Journal: Methods (San Diego, Calif.)

doi: 10.1016/j.ymeth.2017.06.003

Example Agilent Bioanalyzer 2100 trace of 3'-seq library. High quality library should result in a size range distribution as expected from the size range extracted from the gel. Shown is a 3'-seq library that falls in the 150–250 bp size range (labeled). Isolation of a fraction of reads below 175bp is to be expected and will still results in reads that can be mapped to the genome. The peak should be above 130 bp to avoid contamination of adapter-adapter reads (~120 bp). On the right side the densitometry plot with the standard and the sample are shown. On the left an electropherogram of the sample is plotted with fluorescent intensity (FU) on the red y axis and size (nt) on the×axis. The markers run together with the sample are labeled. STD- standard.
Figure Legend Snippet: Example Agilent Bioanalyzer 2100 trace of 3'-seq library. High quality library should result in a size range distribution as expected from the size range extracted from the gel. Shown is a 3'-seq library that falls in the 150–250 bp size range (labeled). Isolation of a fraction of reads below 175bp is to be expected and will still results in reads that can be mapped to the genome. The peak should be above 130 bp to avoid contamination of adapter-adapter reads (~120 bp). On the right side the densitometry plot with the standard and the sample are shown. On the left an electropherogram of the sample is plotted with fluorescent intensity (FU) on the red y axis and size (nt) on the×axis. The markers run together with the sample are labeled. STD- standard.

Techniques Used: Labeling, Isolation

Example of high quality total RNA. Total RNA quality is assessed on the basis of the quality of the predominant signal from rRNA (as labeled). The trace is from high quality total RNA from  Drosophila melanogaster  run on an Agilent Bioanalyzer 2100. Notice that insect 28S rRNA dissociates into two subunits of equal size that co- migrate with the 18S rRNA. The migration of rRNA of other organisms will vary and should be taken into account when validating total RNA quality. Bioanalyzer output is shown. On the right the densitometry plot with the standard and the sample are shown. On the left an electropherogram of the sample is plotted with fluorescent intensity (FU) on the red y axis and size (nt) on the×axis. The marker run together with the sample is labeled. STD- standard.
Figure Legend Snippet: Example of high quality total RNA. Total RNA quality is assessed on the basis of the quality of the predominant signal from rRNA (as labeled). The trace is from high quality total RNA from Drosophila melanogaster run on an Agilent Bioanalyzer 2100. Notice that insect 28S rRNA dissociates into two subunits of equal size that co- migrate with the 18S rRNA. The migration of rRNA of other organisms will vary and should be taken into account when validating total RNA quality. Bioanalyzer output is shown. On the right the densitometry plot with the standard and the sample are shown. On the left an electropherogram of the sample is plotted with fluorescent intensity (FU) on the red y axis and size (nt) on the×axis. The marker run together with the sample is labeled. STD- standard.

Techniques Used: Labeling, Migration, Marker

Optimization of fragmentation time. Agilent Bioanalyzer 2100 traces of the reaction outlined in 2.2.3 stopped at different time intervals. The chemical fragmentation reaction should be stopped when the total RNA peak is around 150–200 nt (10 min) but before the RNA is completely fragmented as shown in the later time points. This step was optimized for fragmentation of Drosophila total RNA and should be optimized when using this protocol to determine 3' ends from total RNA of other organisms. Densitometry of the samples run is shown to the left while electropherograms are shown on the right. Samples are labeled above each lane and on each corresponding inset on the right. The marker, present in each sample, is labeled in the top most panel. STD- standard. FU - fluorescent intensity.
Figure Legend Snippet: Optimization of fragmentation time. Agilent Bioanalyzer 2100 traces of the reaction outlined in 2.2.3 stopped at different time intervals. The chemical fragmentation reaction should be stopped when the total RNA peak is around 150–200 nt (10 min) but before the RNA is completely fragmented as shown in the later time points. This step was optimized for fragmentation of Drosophila total RNA and should be optimized when using this protocol to determine 3' ends from total RNA of other organisms. Densitometry of the samples run is shown to the left while electropherograms are shown on the right. Samples are labeled above each lane and on each corresponding inset on the right. The marker, present in each sample, is labeled in the top most panel. STD- standard. FU - fluorescent intensity.

Techniques Used: Labeling, Marker

Related Articles

Produced:

Article Title: Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy
Article Snippet: .. The TE transcriptome obtained with PGT-AT was of high quality All tested samples produced sufficient quantity and high-quality cDNA for RNAseq, as per BioAnalyzer 2100 (Agilent Technologies, CA) (see Supplementary Fig. ), enabling us to conduct gene expression profiling. ..

Amplification:

Article Title: Gene Expression Analysis of In Vivo Fluorescent Cells
Article Snippet: .. After each amplification round, the RNA was analyzed by Bioanalyzer 2100 (Agilent, USA). .. We typically obtained 100–200 ng and 50–100 µg of amplified RNA after the first and second amplification round, respectively.

Isolation:

Article Title: RNase L amplifies Interferon signaling by inducing PKR-mediated antiviral stress granules
Article Snippet: .. RNA isolation, rRNA cleavage assay and Quantitative real-time PCR Total RNA was isolated from cells using Trizol reagent (Invitrogen), as per manufacture instructions and resolved on RNA chips using Bioanalyzer 2100 (Agilent Technologies) as described previously ( ). .. RNase L cleaved small RNAs, CIP treated RNase L-cleaved small RNAs and control small RNAs were purified as described earlier ( , ).

Real-time Polymerase Chain Reaction:

Article Title: RNase L amplifies Interferon signaling by inducing PKR-mediated antiviral stress granules
Article Snippet: .. RNA isolation, rRNA cleavage assay and Quantitative real-time PCR Total RNA was isolated from cells using Trizol reagent (Invitrogen), as per manufacture instructions and resolved on RNA chips using Bioanalyzer 2100 (Agilent Technologies) as described previously ( ). .. RNase L cleaved small RNAs, CIP treated RNase L-cleaved small RNAs and control small RNAs were purified as described earlier ( , ).

other:

Article Title: Genome-wide profiling of the 3' ends of polyadenylated RNAs
Article Snippet: 5 Determine the quality of prepared total RNA on Bioanalyzer 2100 using the Agilent RNA 6000 Kit.

Article Title: Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs
Article Snippet: RNA Integrity The RNA profile and integrity of all samples (inferred by the RIN) was assessed using the Bioanalyzer 2100 (Agilent Technologies) with the Bio-PicoChip and Bio-SmallChip (see Quantification, Agilent 2100 Bioanalyzer).

Expressing:

Article Title: Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy
Article Snippet: .. The TE transcriptome obtained with PGT-AT was of high quality All tested samples produced sufficient quantity and high-quality cDNA for RNAseq, as per BioAnalyzer 2100 (Agilent Technologies, CA) (see Supplementary Fig. ), enabling us to conduct gene expression profiling. ..

Cleavage Assay:

Article Title: RNase L amplifies Interferon signaling by inducing PKR-mediated antiviral stress granules
Article Snippet: .. RNA isolation, rRNA cleavage assay and Quantitative real-time PCR Total RNA was isolated from cells using Trizol reagent (Invitrogen), as per manufacture instructions and resolved on RNA chips using Bioanalyzer 2100 (Agilent Technologies) as described previously ( ). .. RNase L cleaved small RNAs, CIP treated RNase L-cleaved small RNAs and control small RNAs were purified as described earlier ( , ).

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    Agilent technologies dna chips
    Amplification results using the proposed <t>DNA</t> extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( <t>CSRM60</t> ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).
    Dna Chips, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 15 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    dna chips - by Bioz Stars, 2020-07
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    Agilent technologies agilent 2100 bioanalyzer
    Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using <t>Agilent</t> 2100 <t>Bioanalyzer</t> with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.
    Agilent 2100 Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 6798 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/agilent 2100 bioanalyzer/product/Agilent technologies
    Average 99 stars, based on 6798 article reviews
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    agilent 2100 bioanalyzer - by Bioz Stars, 2020-07
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    Amplification results using the proposed DNA extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( CSRM60 ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).

    Journal: PLoS ONE

    Article Title: A Simple Method to Extract DNA from Hair Shafts Using Enzymatic Laundry Powder

    doi: 10.1371/journal.pone.0069588

    Figure Lengend Snippet: Amplification results using the proposed DNA extraction method (on-chip- electrophoresis results). The size of PCR products are 79–115 bp ( CSRM60 ), 100–124 bp ( INRA035 ). Left to right: L, ladder; 1, sample washing water control ( CSRM60 ); 2, extraction solution (without hair shaft) control ( CSRM60 ); 3, ddH 2 O control ( CSRM60 ); 4, DNA from hair shafts of pure bred Luxi cattle ( CSRM60 ); 5, DNA from liver of beef cattle ( CSRM60 ); 6, sample washing water control ( INRA035 ); 7, extraction solution (without hair shaft) control ( INRA035 ); 8, ddH 2 O control ( INRA035 ); 9, DNA from hair shafts of pure bred Luxi cattle ( INRA035 ); 10, DNA from liver of beef cattle ( INRA035 ).

    Article Snippet: Then, amplification products (locus CSRM60 and INRA035 ) were pipette onto DNA Chips (on-chip-electrophoresis, Agilent DNA 1000 Kit, for use with the Agilent 2100 bioanalyzer) and operated as its Guide described, while the others were visualized under UV light on 1.2% agarose gels by staining with GeneGreen (Tiangen Biotech (Beijing) Co., Ltd.).

    Techniques: Amplification, DNA Extraction, Chromatin Immunoprecipitation, Electrophoresis, Polymerase Chain Reaction

    Comparison of amplification results of DNA extracted from hair shafts using the proposed method and that extracted from liver using commercial Genomic DNA Purification Kit (on-chip-electrophoresis results). The above panel is INRA035 comparison result, sample 6 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 3 is amplification result of liver DNA from beef cattle; The below panel is CSRM60 comparison result, sample 2 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 11 is amplification result of liver DNA from beef cattle.

    Journal: PLoS ONE

    Article Title: A Simple Method to Extract DNA from Hair Shafts Using Enzymatic Laundry Powder

    doi: 10.1371/journal.pone.0069588

    Figure Lengend Snippet: Comparison of amplification results of DNA extracted from hair shafts using the proposed method and that extracted from liver using commercial Genomic DNA Purification Kit (on-chip-electrophoresis results). The above panel is INRA035 comparison result, sample 6 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 3 is amplification result of liver DNA from beef cattle; The below panel is CSRM60 comparison result, sample 2 is amplification result of hair shaft DNA from pure bred Luxi cattle and sample 11 is amplification result of liver DNA from beef cattle.

    Article Snippet: Then, amplification products (locus CSRM60 and INRA035 ) were pipette onto DNA Chips (on-chip-electrophoresis, Agilent DNA 1000 Kit, for use with the Agilent 2100 bioanalyzer) and operated as its Guide described, while the others were visualized under UV light on 1.2% agarose gels by staining with GeneGreen (Tiangen Biotech (Beijing) Co., Ltd.).

    Techniques: Amplification, DNA Purification, Chromatin Immunoprecipitation, Electrophoresis

    Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.

    Journal: BMC Research Notes

    Article Title: Ensuring good quality rna for quantitative real-time pcr isolated from renal proximal tubular cells using laser capture microdissection

    doi: 10.1186/1756-0500-7-62

    Figure Lengend Snippet: Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.

    Article Snippet: RNA integrity number (RIN) RIN was measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit.

    Techniques: Concentration Assay, Produced

    Analyses of the various antibody formats ( A ) To assess the purity and confirm the size of each reagent, the various antibody formats were analyzed by Agilent 2100 bioanalyzer. Proteins were assessed under non-reduced (NR) and reduced conditions (R). 1, IgG; 2, heavy chain; 3, light chain; 4, F(ab)’ 2 ; 5, VH-CH1-hinge; 6, monovalent antibody; 7, hinge-Fc; 8, Fab; 9, light chain and VH-CH1. ( B ) The binding of Hu 15C1 (black circles), monovalent Hu 15C1 (gray triangles), F(ab)’ 2 Hu 15C1 (open circles) and Fab Hu 15C1 (open diamonds) to TLR4 was analyzed by competitive ELISA. To compare the different antibody formats, the same number of binding site was used, i.e., the molar concentration of monovalent and Fab is twice the molar concentration of IgG and F(ab)’ 2 . Results are normalized and expressed as mean ± SD of duplicates. An F test was used to compare the fitted curves of different groups. ns: not significant.

    Journal: mAbs

    Article Title: Maximizing the potency of an anti-TLR4 monoclonal antibody by exploiting proximity to Fcγ receptors

    doi: 10.4161/19420862.2014.975098

    Figure Lengend Snippet: Analyses of the various antibody formats ( A ) To assess the purity and confirm the size of each reagent, the various antibody formats were analyzed by Agilent 2100 bioanalyzer. Proteins were assessed under non-reduced (NR) and reduced conditions (R). 1, IgG; 2, heavy chain; 3, light chain; 4, F(ab)’ 2 ; 5, VH-CH1-hinge; 6, monovalent antibody; 7, hinge-Fc; 8, Fab; 9, light chain and VH-CH1. ( B ) The binding of Hu 15C1 (black circles), monovalent Hu 15C1 (gray triangles), F(ab)’ 2 Hu 15C1 (open circles) and Fab Hu 15C1 (open diamonds) to TLR4 was analyzed by competitive ELISA. To compare the different antibody formats, the same number of binding site was used, i.e., the molar concentration of monovalent and Fab is twice the molar concentration of IgG and F(ab)’ 2 . Results are normalized and expressed as mean ± SD of duplicates. An F test was used to compare the fitted curves of different groups. ns: not significant.

    Article Snippet: The purity and chain composition of each reagent was assessed using an Agilent 2100 bioanalyzer ( ).

    Techniques: Binding Assay, Competitive ELISA, Concentration Assay

    Long-term storage effects on RNA integrity. RIN values for RNA samples isolated from Tempus tubes stored at –80°C until analyzed by Agilent 2100 Bioanalyzer. RIN values for adult blood samples (n = 15 Tempus tubes/year) and RIN values for cord blood samples (n = 6 Tempus tubes/year). Bars represent means ± SE. The average RIN values for adult and cord blood samples were 7.6 ± 0.5 and 7.7 ± 0.7, respectively, and no significant long-term storage related effects on RNA integrity were observed.

    Journal: BMC Research Notes

    Article Title: Long-term storage of blood RNA collected in RNA stabilizing Tempus tubes in a large biobank – evaluation of RNA quality and stability

    doi: 10.1186/1756-0500-7-633

    Figure Lengend Snippet: Long-term storage effects on RNA integrity. RIN values for RNA samples isolated from Tempus tubes stored at –80°C until analyzed by Agilent 2100 Bioanalyzer. RIN values for adult blood samples (n = 15 Tempus tubes/year) and RIN values for cord blood samples (n = 6 Tempus tubes/year). Bars represent means ± SE. The average RIN values for adult and cord blood samples were 7.6 ± 0.5 and 7.7 ± 0.7, respectively, and no significant long-term storage related effects on RNA integrity were observed.

    Article Snippet: The RNA integrity was assessed by an Agilent 2100 Bioanalyzer using the Eukaryote total RNA 6000 Nano LabChip kit and Eukaryote total RNA Nano assay according to the manufacturer’s instructions (Agilent Technologies, Palo Alto, CA).

    Techniques: Isolation