bioanalyzer 2100 (Agilent technologies)

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Agilent technologies bioanalyzer 2100

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)

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1) 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

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

2) 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

3) Product Images from "Reprogramming of Yersinia from Virulent to Persistent Mode Revealed by Complex In Vivo RNA-seq Analysis"

Article Title: Reprogramming of Yersinia from Virulent to Persistent Mode Revealed by Complex In Vivo RNA-seq Analysis

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1004600

Y. pseudotuberculosis infection alters the bacterial composition of the cecum. (A) Representative Bioanalyzer 2100 electrographs and associated gel pictures for replicates of in vitro -derived RNA samples (grown at 26°C and 37°C), in vivo -derived samples of early (isolated from mouse cecal tissue 2 dpi) and persistent infection (isolated from mouse cecal tissue 42 dpi), and uninfected samples (isolated from uninfected mouse cecal tissue). (B) The number of reads mapping to 16S rRNA from different bacteria in non-depleted in vivo -derived samples. Data represent the mean ± SD of the two replicates for each sample group. (C) Relative abundance of different bacterial phyla in samples according to reads mapped to the 16SMicrobial database. The proportions are given as the percent of bacterial phyla identified in specific samples.

Figure Legend Snippet: Y. pseudotuberculosis infection alters the bacterial composition of the cecum. (A) Representative Bioanalyzer 2100 electrographs and associated gel pictures for replicates of in vitro -derived RNA samples (grown at 26°C and 37°C), in vivo -derived samples of early (isolated from mouse cecal tissue 2 dpi) and persistent infection (isolated from mouse cecal tissue 42 dpi), and uninfected samples (isolated from uninfected mouse cecal tissue). (B) The number of reads mapping to 16S rRNA from different bacteria in non-depleted in vivo -derived samples. Data represent the mean ± SD of the two replicates for each sample group. (C) Relative abundance of different bacterial phyla in samples according to reads mapped to the 16SMicrobial database. The proportions are given as the percent of bacterial phyla identified in specific samples.

Techniques Used: Infection, In Vitro, Derivative Assay, In Vivo, Isolation

4) 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 < 0.05 (Welch’s t -test with Bonferroni correction). Pentagons indicate array chips.

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 < 0.05 (Welch’s t -test with Bonferroni correction). Pentagons indicate array chips.

Techniques Used: RNA Extraction, Staining, Expressing, Microarray

5) 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

6) Product Images from "Lactation-Related MicroRNA Expression Profiles of Porcine Breast Milk Exosomes"

Article Title: Lactation-Related MicroRNA Expression Profiles of Porcine Breast Milk Exosomes

Journal: PLoS ONE

doi: 10.1371/journal.pone.0043691

Figure Legend Snippet: Evidence of miRNA-loaded exosomes in porcine breast milk. (A) 3D AFM image of isolated milk exosomes. (B) The line profile of AFM image for a milk exosome. X- and Y-axes are the width and height of a porcine milk exosome, respectively. (C) RNA from porcine breast milk exosomes was detected using Agilent Bioanalyzer 2100.

Techniques Used: Isolation

7) 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

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

8) 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

9) Product Images from "Applicability of Three Alternative Instruments for Food Authenticity Analysis: GMO Identification"

Article Title: Applicability of Three Alternative Instruments for Food Authenticity Analysis: GMO Identification

Journal: Biotechnology Research International

doi: 10.4061/2011/838232

Electropherogram and “gel-like” image of positive control on the Agilent Bioanalyzer 2100. The x -axis on the electropherogram represents amplicon size (bp), whist the y -axis represents the measurement response of fluorescence units (FUs). Amplicons of interest in order of size (bp) are lower marker (15), Zein (80), Lectin (90), CaMV (108) and combined CaMV 35s promoter/NOS terminator (131) amplicons, and the upper marker (1500).

Figure Legend Snippet: Electropherogram and “gel-like” image of positive control on the Agilent Bioanalyzer 2100. The x -axis on the electropherogram represents amplicon size (bp), whist the y -axis represents the measurement response of fluorescence units (FUs). Amplicons of interest in order of size (bp) are lower marker (15), Zein (80), Lectin (90), CaMV (108) and combined CaMV 35s promoter/NOS terminator (131) amplicons, and the upper marker (1500).

Techniques Used: Positive Control, Amplification, Fluorescence, Marker

Bias associated with the amplicons from the positive controls. Figure shows the bias (trueness) associated with the amplicons from the positive controls, across the three instruments of the Bioanalyzer 2100, TapeStation, and MultiNA. The bias is based on the difference between the observed amplicon size per instrument, compared with the theoretical amplicon size based on the sequence information. NOS represents the combined NOS terminator/CaMV 35s promoter amplicon. Bias is calculated on the measurement response of base pairs (bp).

Figure Legend Snippet: Bias associated with the amplicons from the positive controls. Figure shows the bias (trueness) associated with the amplicons from the positive controls, across the three instruments of the Bioanalyzer 2100, TapeStation, and MultiNA. The bias is based on the difference between the observed amplicon size per instrument, compared with the theoretical amplicon size based on the sequence information. NOS represents the combined NOS terminator/CaMV 35s promoter amplicon. Bias is calculated on the measurement response of base pairs (bp).

Techniques Used: Amplification, Sequencing

10) Product Images from "Exosomal miRNAs from Peritoneum Lavage Fluid as Potential Prognostic Biomarkers of Peritoneal Metastasis in Gastric Cancer"

Article Title: Exosomal miRNAs from Peritoneum Lavage Fluid as Potential Prognostic Biomarkers of Peritoneal Metastasis in Gastric Cancer

Journal: PLoS ONE

doi: 10.1371/journal.pone.0130472

Exosomal miRNA expression in malignant ascites (MA), peritoneal lavage fluid (PLF), and cell culture media (CM). Variation and commonality between the samples were examined. Evaluation of total exosomal RNA used a Bioanalyzer 2100. The electropherograms show the size distribution (nucleotides, nt) and fluorescence intensity (FU) of total exosomal RNA isolated from CM, MA, and PLF. The lowest spike (around 25 nt) in each sample is the marker of the Agilent RNA 6000 Pico kit.

Figure Legend Snippet: Exosomal miRNA expression in malignant ascites (MA), peritoneal lavage fluid (PLF), and cell culture media (CM). Variation and commonality between the samples were examined. Evaluation of total exosomal RNA used a Bioanalyzer 2100. The electropherograms show the size distribution (nucleotides, nt) and fluorescence intensity (FU) of total exosomal RNA isolated from CM, MA, and PLF. The lowest spike (around 25 nt) in each sample is the marker of the Agilent RNA 6000 Pico kit.

Techniques Used: Expressing, Cell Culture, Fluorescence, Isolation, Marker

11) Product Images from "Human breast milk as a source of deoxyribonucleic acid for amplification"

Article Title: Human breast milk as a source of deoxyribonucleic acid for amplification

Journal:

doi: 10.1177/0091270010370847

Representative chromatograms of PCR analysis of milk DNA samples PCR products were analyzed on the Agilent Bioanalyzer 2100 DNA 1,000 chip. The chromatograms are representative of samples that showed no amplification (top), weak amplification (middle), or strong amplification (bottom). Y-axis is the fluorescence detection of the PCR product. X-axis is the size of the amplicon in nucleotides. The first and last peaks are the internal standard markers (15 and 1500 nucleotides).

Figure Legend Snippet: Representative chromatograms of PCR analysis of milk DNA samples PCR products were analyzed on the Agilent Bioanalyzer 2100 DNA 1,000 chip. The chromatograms are representative of samples that showed no amplification (top), weak amplification (middle), or strong amplification (bottom). Y-axis is the fluorescence detection of the PCR product. X-axis is the size of the amplicon in nucleotides. The first and last peaks are the internal standard markers (15 and 1500 nucleotides).

Techniques Used: Polymerase Chain Reaction, Chromatin Immunoprecipitation, Amplification, Fluorescence

12) Product Images from "Effects of Ethanol and NAP on Cerebellar Expression of the Neural Cell Adhesion Molecule L1"

Article Title: Effects of Ethanol and NAP on Cerebellar Expression of the Neural Cell Adhesion Molecule L1

Journal: PLoS ONE

doi: 10.1371/journal.pone.0024364

RNA quality, assay reliability, and validation of endogenous controls. Total RNA quality was assessed using an Agilent Bioanalyzer 2100 and endogenous controls were validated for RT-qPCR and Western blot. A) Generated gel images show representative slice, CGN, and astrocyte samples with and without 24-hr ethanol treatment. B) A standard curve was performed using a dilution series of purified L1 template. Increases in template concentration result in decreasing Cq values, as expected for a well-functioning qPCR assay (n = 4). C) 18S Cq values are shown for all tissue/cell types with and without ethanol treatment. D) Representative Western blots for β-tubulin are shown for each sample type with and without 24-hr ethanol treatment. All bars (C, D) show the mean + SEM of 4 independent experiments.

Figure Legend Snippet: RNA quality, assay reliability, and validation of endogenous controls. Total RNA quality was assessed using an Agilent Bioanalyzer 2100 and endogenous controls were validated for RT-qPCR and Western blot. A) Generated gel images show representative slice, CGN, and astrocyte samples with and without 24-hr ethanol treatment. B) A standard curve was performed using a dilution series of purified L1 template. Increases in template concentration result in decreasing Cq values, as expected for a well-functioning qPCR assay (n = 4). C) 18S Cq values are shown for all tissue/cell types with and without ethanol treatment. D) Representative Western blots for β-tubulin are shown for each sample type with and without 24-hr ethanol treatment. All bars (C, D) show the mean + SEM of 4 independent experiments.

Techniques Used: Quantitative RT-PCR, Western Blot, Generated, Purification, Concentration Assay, Real-time Polymerase Chain Reaction

13) Product Images from "Applicability of Three Alternative Instruments for Food Authenticity Analysis: GMO Identification"

Article Title: Applicability of Three Alternative Instruments for Food Authenticity Analysis: GMO Identification

Journal: Biotechnology Research International

doi: 10.4061/2011/838232

Techniques Used: Positive Control, Amplification, Fluorescence, Marker

Techniques Used: Amplification, Sequencing

14) Product Images from "Mixed Triple: Allied Viruses in Unique Recent Isolates of Highly Virulent Type 2 Bovine Viral Diarrhea Virus Detected by Deep Sequencing"

Article Title: Mixed Triple: Allied Viruses in Unique Recent Isolates of Highly Virulent Type 2 Bovine Viral Diarrhea Virus Detected by Deep Sequencing

Journal:

doi: 10.1128/JVI.00620-14

Agilent Bioanalyzer 2100 analyses (with a DNA 7500 chip) of PCR products. (Upper panels) Gel view of Agilent traces. Bands representing dup + and dup − genomes are marked by arrows labeled accordingly. (Lower panels) Bar plots of relative quantities

Figure Legend Snippet: Agilent Bioanalyzer 2100 analyses (with a DNA 7500 chip) of PCR products. (Upper panels) Gel view of Agilent traces. Bands representing dup + and dup − genomes are marked by arrows labeled accordingly. (Lower panels) Bar plots of relative quantities

Techniques Used: Chromatin Immunoprecipitation, Polymerase Chain Reaction, Labeling

15) 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

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

16) Product Images from "New miRNA labeling method for bead-based quantification"

Article Title: New miRNA labeling method for bead-based quantification

Journal: BMC Molecular Biology

doi: 10.1186/1471-2199-11-44

Schematic representation of miRNA labeling method for bead based quantification . All protocol steps and quality checking with Agilent Bioanalyzer 2100 and gel electrophoresis (2% agarose) are schematically represented: starting material (RNA

Figure Legend Snippet: Schematic representation of miRNA labeling method for bead based quantification . All protocol steps and quality checking with Agilent Bioanalyzer 2100 and gel electrophoresis (2% agarose) are schematically represented: starting material (RNA

Techniques Used: Labeling, Nucleic Acid Electrophoresis

17) Product Images from "Successful Application of Microarray Technology to Microdissected Formalin-Fixed, Paraffin-Embedded Tissue"

Article Title: Successful Application of Microarray Technology to Microdissected Formalin-Fixed, Paraffin-Embedded Tissue

Journal:

doi: 10.2353/jmoldx.2007.060004

$Electropherogram of total RNA obtained from cells following LCM. RNA extracted from LCM FFPE or frozen tissue was loaded on a Bioanalyzer Pico RNA Chip and fractionated in an Agilent Bioanalyzer 2100. Sample number and year of collection are indicated$
Figure Legend Snippet: Electropherogram of total RNA obtained from cells following LCM. RNA extracted from LCM FFPE or frozen tissue was loaded on a Bioanalyzer Pico RNA Chip and fractionated in an Agilent Bioanalyzer 2100. Sample number and year of collection are indicated

Techniques Used: Laser Capture Microdissection, Formalin-fixed Paraffin-Embedded, Chromatin Immunoprecipitation

$Comparative analysis of total RNA obtained by LCM and from scraped tissue. One microliter of RNA extracted from frozen or FFPE tissue was loaded on a Bioanalyzer Pico RNA Chip and fractionated in an Agilent Bioanalyzer 2100. 18S and 28S ribosomal RNA$
Figure Legend Snippet: Comparative analysis of total RNA obtained by LCM and from scraped tissue. One microliter of RNA extracted from frozen or FFPE tissue was loaded on a Bioanalyzer Pico RNA Chip and fractionated in an Agilent Bioanalyzer 2100. 18S and 28S ribosomal RNA

Techniques Used: Laser Capture Microdissection, Formalin-fixed Paraffin-Embedded, Chromatin Immunoprecipitation

18) Product Images from "Hybrid Capture and Next-Generation Sequencing Identify Viral Integration Sites from Formalin-Fixed, Paraffin-Embedded Tissue"

Article Title: Hybrid Capture and Next-Generation Sequencing Identify Viral Integration Sites from Formalin-Fixed, Paraffin-Embedded Tissue

Journal:

doi: 10.1016/j.jmoldx.2011.01.006

Validating biotin-14-dCTP incorporation by a bind and boil method. The biotin–streptavidin dissociation constant (kD) is on the order of 4 × 10−14 mol/L. However, boiling the biotin-steptavidin complexes in the presence of SDS releases these noncovalent complexes. To validate the incorporation of biotin-14-dCTP during the PCR, we assayed the supernatant of our PCR “bait” solution after mixing with Dynal M-280 beads. If biotin-14-dCTP did not incorporate during the PCR, we would expect the supernatant to contain PCR-amplified DNA. To assay the supernatant, we performed a buffer exchange using AmpureXP beads, eluted in water, and evaluated the supernatant of PCR on the Agilent BioAnalyzer 2100 High Sensitivity DNA chip (red dotted line). The Dynal M-280 beads were boiled in 0.1% SDS, and this supernatant was assayed for PCR products (dotted blue line). A second boil treatment was performed, and this supernatant was assayed for the presence of PCR products (dotted green line). FU, fluorescent units; nt, nucleotides.

Figure Legend Snippet: Validating biotin-14-dCTP incorporation by a bind and boil method. The biotin–streptavidin dissociation constant (kD) is on the order of 4 × 10−14 mol/L. However, boiling the biotin-steptavidin complexes in the presence of SDS releases these noncovalent complexes. To validate the incorporation of biotin-14-dCTP during the PCR, we assayed the supernatant of our PCR “bait” solution after mixing with Dynal M-280 beads. If biotin-14-dCTP did not incorporate during the PCR, we would expect the supernatant to contain PCR-amplified DNA. To assay the supernatant, we performed a buffer exchange using AmpureXP beads, eluted in water, and evaluated the supernatant of PCR on the Agilent BioAnalyzer 2100 High Sensitivity DNA chip (red dotted line). The Dynal M-280 beads were boiled in 0.1% SDS, and this supernatant was assayed for PCR products (dotted blue line). A second boil treatment was performed, and this supernatant was assayed for the presence of PCR products (dotted green line). FU, fluorescent units; nt, nucleotides.

Techniques Used: Polymerase Chain Reaction, Amplification, Buffer Exchange, Chromatin Immunoprecipitation

19) 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

20) Product Images from "Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila"

Article Title: Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila

Journal: Nature Communications

doi: 10.1038/ncomms12128

$Identification of the Drosophila RNA interactome. ( a ) Direct RNA binders are CL to mRNAs in living Drosophila embryos, which are subsequently lysed under denaturing conditions. mRNA-protein complexes are purified by hybridization with oligo(dT) magnetic beads and a series of stringent washes. Proteins are released by RNase treatment and are ready for MS analysis. ( b ) Analysis of total and oligo(dT) by Bioanalyzer 2100 captured RNA shows depletion of abundant ncRNAs. ( c ) Multifold enrichment of polyadenylated gapdh and ts mRNAs in oligo(dT) bound fractions confirmed by RT-qPCR. On the x axis are indicated the samples in which the amounts of the different RNAs were measured: Input noCL, input CL, eluate noCL, eluate CL. The y axis represents the fold enrichment of RNA amounts in the different samples. RNA amounts in noCL input were defined as 1. Error bars: s.d. See Supplementary Table 1 for information on oligonucleotides used for the analysis. ( d ) Protein profiles of total embryo and RNA-bound fractions. ( e ) Analysis of total embryo lysates and oligo(dT) bound fractions by western blotting with antibodies against Vasa, eIF4E, Pabp2, PABPC, Hrp48, tubulin, Y14 and H3. Lysis at 60 °C and 12.5 mM DTT ensures that tubulin background is removed. See Supplementary Table 2 for antibody information. ( f ) Replicated samples prepared from pre- (0–1 h) and post-MZT (4.5–5.5 h) embryos are mixed to generate three aggregate CL and noCL (control) samples. Proteins are partially digested, TMT labelled and quantified by MS. ( g ) Scatter plot showing protein abundance ratios CL/noCL in two replicates. Red dots represent proteins significantly enriched in CL samples. ( h ) Venn diagram comparing numbers of detected and significantly enriched proteins.$
Figure Legend Snippet: Identification of the Drosophila RNA interactome. ( a ) Direct RNA binders are CL to mRNAs in living Drosophila embryos, which are subsequently lysed under denaturing conditions. mRNA-protein complexes are purified by hybridization with oligo(dT) magnetic beads and a series of stringent washes. Proteins are released by RNase treatment and are ready for MS analysis. ( b ) Analysis of total and oligo(dT) by Bioanalyzer 2100 captured RNA shows depletion of abundant ncRNAs. ( c ) Multifold enrichment of polyadenylated gapdh and ts mRNAs in oligo(dT) bound fractions confirmed by RT-qPCR. On the x axis are indicated the samples in which the amounts of the different RNAs were measured: Input noCL, input CL, eluate noCL, eluate CL. The y axis represents the fold enrichment of RNA amounts in the different samples. RNA amounts in noCL input were defined as 1. Error bars: s.d. See Supplementary Table 1 for information on oligonucleotides used for the analysis. ( d ) Protein profiles of total embryo and RNA-bound fractions. ( e ) Analysis of total embryo lysates and oligo(dT) bound fractions by western blotting with antibodies against Vasa, eIF4E, Pabp2, PABPC, Hrp48, tubulin, Y14 and H3. Lysis at 60 °C and 12.5 mM DTT ensures that tubulin background is removed. See Supplementary Table 2 for antibody information. ( f ) Replicated samples prepared from pre- (0–1 h) and post-MZT (4.5–5.5 h) embryos are mixed to generate three aggregate CL and noCL (control) samples. Proteins are partially digested, TMT labelled and quantified by MS. ( g ) Scatter plot showing protein abundance ratios CL/noCL in two replicates. Red dots represent proteins significantly enriched in CL samples. ( h ) Venn diagram comparing numbers of detected and significantly enriched proteins.

Techniques Used: Purification, Hybridization, Magnetic Beads, Mass Spectrometry, Quantitative RT-PCR, Western Blot, Lysis

Methylation Sequencing:

Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Article Snippet: Paragraph title: Targeted bisulfite sequencing with the Methyl-Seq technology ... The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing.

DNA Extraction:

Article Title: The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity
Article Snippet: PCR product was PAGE purified from 8% TBE polyacrylamide gels, extracted overnight using DNA extraction buffer, and isopropanol precipitated overnight at −80°C. .. DNA was measured and quality controlled on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid Facility.

Article Title: Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next Generation Sequencing
Article Snippet: Relevant to the current work, capture probes incorporate viral genome sequence for HPV strains 16 and 18 (GenBank IDs and , respectively). .. During DNA isolation and library preparation, DNA concentration was measured by fluorometry, DNA quality was assessed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay, and DNA size was determined by Experion automated electrophoresis system (BioRad, Hercules CA) or by Agilent TapeStation. .. Sequencing was then performed using a HiSeq2000 sequencer (Illumina Inc, San Diego CA).

Amplification:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: The cleaned products were pooled together (2 μl of each reaction) to create a single pooling of each separate DNA sample (44 individual samples containing 26 amplified genomic regions spanning 9 genes). .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
Article Snippet: Concentration of amplified cDNA was measured using NanoDrop 2000 spectrophotometer. cDNA libraries were then prepared using Ion Plus Fragment library Kit (Ion Torrent, Life Technologies) following manufacturer's protocols. cDNA libraries were purified using Magnetic Bead Cleanup Module (Ion Torrent, Life Technologies). .. The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit).

Article Title: The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity
Article Snippet: 1 uL of library was used for PCR amplification with Phusion High-Fidelity DNA Polymerase (Thermo Fisher, catalog no. F530S) (98°C 30s, 98°C 10s, 65°C 10s, 72°C 5s) for 10–11 cycles using the ribosome profiling library PCR forward primer and indexed reverse primers (see table). .. DNA was measured and quality controlled on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid Facility.

Article Title: QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments
Article Snippet: Finally, the DNA was again amplified and barcode sequences where attached to the sequences. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies).

Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Article Snippet: A further amplification step was performed to add barcode sequences for sample pooling and sequencing analysis via the Illumina HiSeq2000 platform. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing.

Article Title: Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci
Article Snippet: A total of 50,000 nuclei were subjected to Tn5-mediated transposition for 1 h and tagmented DNA was amplified and purified as previously reported. .. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed and subjected to a lane of Illumina HiSeq 2500 sequencing.

Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
Article Snippet: Briefly, 100–500 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 10 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

Article Title: Vector transmission regulates immune control of Plasmodium virulence
Article Snippet: Paragraph title: Amplification-free RNA-seq libraries ... Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR.

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. The captured regions were then bound to Streptavidin T1 magnetic beads (Life Technologies, Inc.) and washed to remove any non-specific bound products.

Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
Article Snippet: Following end repair and 3′ adenylation, indexing adapters were ligated to the fragment ends. .. Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). .. Each DNA library was quantitated using quantitative PCR (KAPA Biosystems) prior to normalization.

Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
Article Snippet: We amplified the bacterial 16S rRNA gene V1-V2 hypervariable region using the forward primer 8F fused with the Ion Torrent Adaptor A sequence and one of 23 unique 10 base pair barcodes and reverse primer 357R fused with the Ion Torrent Adaptor P1 from the each donor and sample type [ ]. .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA).

Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
Article Snippet: Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality. .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality.

Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
Article Snippet: In brief, poly‐A+ RNA was isolated using poly‐T oligo‐attached magnetic beads followed by fragmentation and first and second cDNA strand synthesis. cDNA 3′ ends were adenylated and the adapters were ligated. .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies). .. Libraries were sequenced on a HiSeq2500 sequencer (Illumina), 60‐base single reads were generated.

Electrophoresis:

Article Title: Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci
Article Snippet: Libraries were subjected to an additional electrophoresis step on an E-Gel EX 2% agarose gel (Invitrogen), and gel fragments correlating to 100–1,000 bp were excised and purified. .. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed and subjected to a lane of Illumina HiSeq 2500 sequencing.

Incubation:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: On ice, 5 μl of the PCR reactions were mixed with 2 μl ExoSAP-IT solution and incubated at 37 °C for 15 min, then at 80 °C for 15 min. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

Article Title: Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci
Article Snippet: This suspension was incubated with rocking at 4 °C for 10 min and then homogenized via 15 loose strokes in a glass dounce. .. The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed and subjected to a lane of Illumina HiSeq 2500 sequencing.

Formalin-fixed Paraffin-Embedded:

Article Title: Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next Generation Sequencing
Article Snippet: DNA was extracted from fresh frozen tissue samples (16 cases) or from FFPE tissue sections (5 cases) using either the Gentra Puregene Tissue Kit (QIAGEN, Valencia CA) or the Maxwell 16 DNA purification platform (Promega Corp, Madison, WI), and then fragmented by sonication. .. During DNA isolation and library preparation, DNA concentration was measured by fluorometry, DNA quality was assessed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay, and DNA size was determined by Experion automated electrophoresis system (BioRad, Hercules CA) or by Agilent TapeStation.

Ex Vivo:

Article Title: Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci
Article Snippet: Paragraph title: Ex vivo ATAC-seq analysis in coronary artery tissues ... The quality of the library preparation was determined by evaluation of the electropherogram traces from an Agilent 2100 Bioanalyzer DNA High Sensitivity, and libraries demonstrating appropriate nucleosomal enrichment were multiplexed and subjected to a lane of Illumina HiSeq 2500 sequencing.

RNA Binding Assay:

Article Title: The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity
Article Snippet: Samples were then circularized with CircLigase (Illumina, catalog no. CL4115K) in a 20 uL reaction (15 uL cDNA, 2 uL 10x CircLigase Buffer, 1 uL 1 mM ATP, 1 uL MnCl2 , 1 uL CircLigase) for 12 hours at 60°C and subsequently purified by Zymo RNA Clean & Concentrator 5 columns (100 uL sample, 200 uL RNA binding buffer, 300 uL 100% ethanol) and eluted with 12 uL nuclease free water. .. DNA was measured and quality controlled on the Agilent 2100 Bioanalyzer (High-Sensitivity DNA) by the Stanford Protein and Nucleic Acid Facility.

Flow Cytometry:

Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
Article Snippet: Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). .. Each DNA library was quantitated using quantitative PCR (KAPA Biosystems) prior to normalization.

Ligation:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: The NEBNext Ultra™ DNA Library Prep Kit for Illumina (E7370) and NEBNext Mutiplex Oligos for Illumina dual index kit (E7600) were used for end repair and adaptor ligation and quantification (bar coding for multiplex sequencing) using the standard manufacturer protocols. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

Article Title: Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next Generation Sequencing
Article Snippet: Resultant DNA fragments were then subjected to repair and end-polishing (blunt-end or A-overhang), before ligation of custom, single-end adapters. .. During DNA isolation and library preparation, DNA concentration was measured by fluorometry, DNA quality was assessed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay, and DNA size was determined by Experion automated electrophoresis system (BioRad, Hercules CA) or by Agilent TapeStation.

Article Title: Vector transmission regulates immune control of Plasmodium virulence
Article Snippet: Sequencing templates were prepared by mixing 15μl cDNA, 5μl 33μM adaptors (based on the published adaptor with the addition of barcode sequences; oligos supplied by Integrated DNA Technologies), 25μl Quick Ligation buffer and 5μl Quick DNA ligase (both from New England Biolabs) and incubating for 15 minutes at 25°C. .. Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR.

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: 3 μg of genomic DNA was fragmented to a size range of 150-200 bp followed by end repair, adaptor ligation, and low cycle (5) PCR. .. Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.).

Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
Article Snippet: The RNA products from the controlled fragmentation step were used to prepare the strand-specific metatranscriptomic library, following the manufacturer’s instruction of Apollo 324 PrepX mRNA library protocol (IntegenX), which is based on directional RNA adaptor ligation. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies).

Methylation:

Article Title: QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments
Article Snippet: The methylated adapter was then ligated to the fragmented DNA. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies).

Cell Culture:

Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
Article Snippet: To evaluate transcripts generated by the region of the QPD duplication, including the QPD breakpoint, approximately 1 μg of total RNA/sample from 3 control and 3 QPD samples of day 14 cultured megakaryocytes and affinity purified granulocytes was prepared. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

Generated:

Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
Article Snippet: To evaluate transcripts generated by the region of the QPD duplication, including the QPD breakpoint, approximately 1 μg of total RNA/sample from 3 control and 3 QPD samples of day 14 cultured megakaryocytes and affinity purified granulocytes was prepared. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
Article Snippet: Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies). .. Sequencing of 141-nt single-end reads was performed on one lane of Illumina 2500 HiSeq platform with Illumina’s Truseq Rapid SBS chemistry.

DNA HS Assay:

Sequencing:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: The NEBNext Ultra™ DNA Library Prep Kit for Illumina (E7370) and NEBNext Mutiplex Oligos for Illumina dual index kit (E7600) were used for end repair and adaptor ligation and quantification (bar coding for multiplex sequencing) using the standard manufacturer protocols. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
Article Snippet: The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit). .. During the next step, clonal amplification was performed using Ion PI™ Template OT2 200 Kit v3 and Ion OneTouch™ 2 system (Life Technologies) in accordance with manufacturer's recommendations.

Article Title: Noninvasive monitoring of infection and rejection after lung transplantation
Article Snippet: Paragraph title: Sequencing Library Preparation and Sequencing. ... Libraries were characterized using the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit) or the AATI fragment analyzer, quantified by quantitative PCR, and sequenced (Illumina HiSeq 2000, HiSeq 2500, or NextSeq 500; 1 × 50 bp or 2 × 100 bp).

Article Title: Identification of Human Papillomavirus Infection in Cancer Tissue by Targeted Next Generation Sequencing
Article Snippet: Paragraph title: DNA Isolation, Library Preparation, and Sequencing ... During DNA isolation and library preparation, DNA concentration was measured by fluorometry, DNA quality was assessed using the Agilent 2100 Bioanalyzer high sensitivity DNA assay, and DNA size was determined by Experion automated electrophoresis system (BioRad, Hercules CA) or by Agilent TapeStation.

Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Article Snippet: A further amplification step was performed to add barcode sequences for sample pooling and sequencing analysis via the Illumina HiSeq2000 platform. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing. .. Adapter sequences in paired-end Methyl-Seq reads were trimmed using trim_galore version 0.4.0 and then aligned using bismark v0.10.0 based on bowtie2 version 2.2.1 with default parameters [ , ].

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: Paragraph title: Whole exome sequencing (WES) ... Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.).

Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
Article Snippet: Paragraph title: Whole-Genome Sequencing (WGS) ... Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies).

Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
Article Snippet: Before sequencing, the total RNA sample was analyzed on the Agilent 2100 BioAnalyzer system using RNA 6000 Nano kit. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies).

Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
Article Snippet: The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA). .. Libraries were quantified using both the Qubit® Fluorometer (Life Technologies, USA) and the qPCR-based NEBNext library quantification kit (New England BioLabs, UK).

Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
Article Snippet: The total coding region of mtDNA was screened by Sanger sequencing using ABI Prism 3500 DNA Sequencer (Applied Biosystems, Foster City, USA); the obtained sequences were compared with the mitomap databases using NCBI's Blast® application, while mtDNA deletion was investigated with long PCRs using Phusion High‐Fidelity DNA Polymerase (Finnzyme, Vanta, Finland). .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality.

Sonication:

Affinity Purification:

Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
Article Snippet: To evaluate transcripts generated by the region of the QPD duplication, including the QPD breakpoint, approximately 1 μg of total RNA/sample from 3 control and 3 QPD samples of day 14 cultured megakaryocytes and affinity purified granulocytes was prepared. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

Binding Assay:

Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
Article Snippet: In brief, poly(A) RNA was purified from 1 µg of total RNA using two serial rounds of binding to oligo(dT) magnetic particles; then, fragmented RNA was reverse transcribed to generate cDNA. .. The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA).

Multiplexing:

Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
Article Snippet: An Illumina-specific adaptor was sequentially ligated to the 3′ end of cDNA fragments, purified using the AMPure XP beads (Beckman Coulter, Brea, CA, USA), and finally PCR-amplified (13 cycles) using an appropriate indexing primer to allow further samples multiplexing. .. The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA).

RNA Sequencing Assay:

Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Article Snippet: Paragraph title: RNA-seq: data generation and bioinformatics ... One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
Article Snippet: Paragraph title: Illumina RNA-sequencing and transcriptome library construction ... Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol.

Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
Article Snippet: Paragraph title: RNA-seq ... 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA).

Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
Article Snippet: Paragraph title: Directional RNA-Sequencing. ... Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies).

Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
Article Snippet: Paragraph title: Library preparation and RNA-Seq analysis ... The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA).

Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
Article Snippet: Paragraph title: Library preparation and RNA sequencing ... After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies).

RNA HS Assay:

Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Article Snippet: Concentration was measured by Qubit RNA HS Assay on a Qubit fluorometer (ThermoFisher). .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

Magnetic Beads:

Article Title: QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments
Article Snippet: Following the capturing of the RNA-DNA hybrids using streptavidine-coated magnetic beads, the DNA was separated from the beads, eluted and bisulfite converted using the EpiTECT Kit (Qiagen). .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies).

Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Article Snippet: Following the capturing of the RNA-DNA hybrids using streptavidine-coated magnetic beads, DNA was separated from the beads, eluted, and bisulfite-treated using the EpiTect Bisulfite Kit. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing.

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. 750 ng of purified library was then hybridized to the SureSelectXT Human All Exon 50 Mb library for 18 hours at 65°C.

Isolation:

Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Article Snippet: Ribonucleic acid (RNA) was isolated from peripheral blood leukocytes using QIAsymphony PAXgene Blood RNA Kit (Qiagen) and sequenced using the Illumina Hi-Seq 2500. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

Size-exclusion Chromatography:

Purification:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: Clean-up of adaptor-ligated DNA was performed using Agencourt AMPure XP - PCR Purification ( ) following the manufacturer’s standard protocol. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

Article Title: Noninvasive monitoring of infection and rejection after lung transplantation
Article Snippet: Sequencing libraries were prepared from purified plasma DNA using the NEBNext DNA Library Prep Master Mix Set for Illumina with standard Illumina indexed adapters (IDT) or using a microfluidics-based automated library preparation platform (Mondrian ST; Ovation SP Ultralow Library Systems). .. Libraries were characterized using the Agilent 2100 Bioanalyzer (High Sensitivity DNA Kit) or the AATI fragment analyzer, quantified by quantitative PCR, and sequenced (Illumina HiSeq 2000, HiSeq 2500, or NextSeq 500; 1 × 50 bp or 2 × 100 bp).

Article Title: QSEA—modelling of genome-wide DNA methylation from sequencing enrichment experiments
Article Snippet: The bisulfite-treated libraries were PCR amplified and purified. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies).

Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Article Snippet: The bisulfite-converted DNA libraries were PCR-amplified and purified. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing.

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: 3 μg of genomic DNA was fragmented to a size range of 150-200 bp followed by end repair, adaptor ligation, and low cycle (5) PCR. .. Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. 750 ng of purified library was then hybridized to the SureSelectXT Human All Exon 50 Mb library for 18 hours at 65°C.

Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
Article Snippet: Resulting amplicons were purified on a 2 % agarose gel stained with SYBR Safe (Invitrogen, Carlsbad, CA) using the MinElute PCR Purification kit (Qiagen, Valencia, CA). .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA). .. Samples were pooled into equimolar proportions and sequenced on 314 chips using an Ion Torrent PGM according to manufacturer’s instructions (Life Technologies, Grand Island, NY) [ ].

Polymerase Chain Reaction:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: Clean-up of adaptor-ligated DNA was performed using Agencourt AMPure XP - PCR Purification ( ) following the manufacturer’s standard protocol. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

Article Title: Epigenomic profiling of non-small cell lung cancer xenografts uncover LRP12 DNA methylation as predictive biomarker for carboplatin resistance
Article Snippet: The bisulfite-converted DNA libraries were PCR-amplified and purified. .. The indexed DNA pool was analyzed with the 2100 Bioanalyzer High Sensitivity DNA assay (Agilent Technologies) prior to sequencing.

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: 3 μg of genomic DNA was fragmented to a size range of 150-200 bp followed by end repair, adaptor ligation, and low cycle (5) PCR. .. Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.).

Polyacrylamide Gel Electrophoresis:

cDNA Library Assay:

Agarose Gel Electrophoresis:

Chromatin Immunoprecipitation:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: Clean-up of adaptor-ligated DNA was performed using Agencourt AMPure XP - PCR Purification ( ) following the manufacturer’s standard protocol. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ]. .. Indexed libraries were pooled, and paired-end multiplexed sequencing (2 × 310 bp) was performed on an Illumina Miseq platform using MiSeq Reagent Kit v3.

Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
Article Snippet: D, September 2012), following the recommended protocol. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol. .. Libraries were pooled in equimolar quantities and paired end sequenced on an Illumina 2500 platform using a Rapid Run Mode Flow Cell and the V3 sequencing chemistry following Illumina’s recommended protocol to generate paired-end reads of 150-bases in length (150 × 2).

Article Title: Vector transmission regulates immune control of Plasmodium virulence
Article Snippet: Excess adaptors were removed with 2 rounds of clean up with 50μl of Agencourt AMPure XP Beads (Beckman Coulter). .. Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR. .. A pool of the 5 indexed libraries was sequenced on an Illumina HiSeq2000, with 100bp paired-end reads.

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: 3 μg of genomic DNA was fragmented to a size range of 150-200 bp followed by end repair, adaptor ligation, and low cycle (5) PCR. .. Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. 750 ng of purified library was then hybridized to the SureSelectXT Human All Exon 50 Mb library for 18 hours at 65°C.

Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
Article Snippet: First pre‐capture genomic library was prepared using 1 μg of highly purified genomic DNA. .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality. .. Next, during exome enrichment step, individual pre‐captured libraries were hybridized to biotinylated NimbleGen SeqCap EZ Human Exome Library for 68–70 h at 47°C.

Software:

Article Title: Whole-genome sequencing of a malignant granular cell tumor with metabolic response to pazopanib
Article Snippet: Following purification, the fragmented DNA was PCR amplified for five cycles, purified, and validated for appropriate size on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies). .. Libraries were loaded and clustered to individual lanes of a HiSeq Flow Cell using an Illumina cBot (TruSeq PE Cluster Kit v3), followed by 2 × 100 cycle paired-end WGS on a HiSeq2000 sequencer according to the manufacturer's recommended protocol (Illumina).

Real-time Polymerase Chain Reaction:

Article Title: Genomic profiling is predictive of response to cisplatin treatment but not to PI3K inhibition in bladder cancer patient-derived xenografts
Article Snippet: Libraries were purified and validated for appropriate size (225-275 bp) on a 2100 Bioanalyzer High Sensitivity DNA chip (Agilent Technologies, Inc.). .. Eluted library underwent a second 11 cycle PCR amplification using Herculase II Fusion Polymerase (Agilent Technologies, Inc.) to add sample specific barcodes necessary for multiplexing.

Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
Article Snippet: The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA). .. In the presence of adaptor-dimers (Electropherogram’s peak at 100 to 150-bp), another round of magnetic beads purification was performed.

Multiplex Assay:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: The NEBNext Ultra™ DNA Library Prep Kit for Illumina (E7370) and NEBNext Mutiplex Oligos for Illumina dual index kit (E7600) were used for end repair and adaptor ligation and quantification (bar coding for multiplex sequencing) using the standard manufacturer protocols. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

Selection:

Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
Article Snippet: Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol.

Sample Prep:

Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
Article Snippet: Library preparation was performed with the Illumina TruSeq RNA Sample Preparation V2 Guide (Rev. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol.

Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
Article Snippet: Genomic DNA library preparation was performed by using TruSeq® DNA Sample Prep Kit v2‐Set A (Illumina), followed by NimbleGen SeqCap EZ Human Exome Library v3.0 Kit exome enrichment (Roche). .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality.

Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
Article Snippet: Total RNA (500 ng) was used to prepare barcoded RNA sequencing libraries using the TruSeq RNA sample preparation kit v2 (Illumina) as described before (Villa‐Bellosta et al , ). .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies).

Next-Generation Sequencing:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: Paragraph title: Bisulphite conversion of DNA and targeted Illumina NGS ... Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ].

Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
Article Snippet: Paragraph title: Total RNA preparation and cDNA library construction for NGS ... The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit).

Article Title: Fingerprinting of Proteins that Mediate Quagga Mussel Adhesion using a De Novo Assembled Foot Transcriptome
Article Snippet: Next-generation sequencing was completed at The Centre for Applied Genomics (TCAG) at the Hospital for Sick Children in Toronto, Ontario. .. Libraries were checked on a Bioanalyzer 2100 DNA High Sensitivity Chip (Agilent Technologies) to check for size and quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit (KAPA Biosystems) following the manufacturer’s recommended protocol.

Article Title: Progerin accelerates atherosclerosis by inducing endoplasmic reticulum stress in vascular smooth muscle cells
Article Snippet: After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies). .. After PCR library amplification, its size was tested using the Agilent 2100 Bioanalyzer DNA 1000 chip and concentration was measured in a Qubit fluorometer (Life Technologies).

Random Hexamer Labeling:

Article Title: Vector transmission regulates immune control of Plasmodium virulence
Article Snippet: First strand cDNA was synthesised with Random Hexamer primers and SuperScript II Reverse Transcriptase (Life Technologies), following the manufacturer’s instructions. .. Final libraries were eluted in 30μl water, visualised on an Agilent Bioanalyzer 2100 High Sensitivity DNA chip and quantified by qPCR.

Spectrophotometry:

Concentration Assay:

Article Title: SMYD2 promoter DNA methylation is associated with abdominal aortic aneurysm (AAA) and SMYD2 expression in vascular smooth muscle cells
Article Snippet: Clean-up of adaptor-ligated DNA was performed using Agencourt AMPure XP - PCR Purification ( ) following the manufacturer’s standard protocol. .. Each of the adaptor ligated, bar-coded DNA samples was ran on an Agilent 2100 Bioanalyzer Instrument (expert High-Sensitivity DNA chip) to assess sample DNA concentration and the presence and distribution of correct fragment sizes [ ]. .. Indexed libraries were pooled, and paired-end multiplexed sequencing (2 × 310 bp) was performed on an Illumina Miseq platform using MiSeq Reagent Kit v3.

Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Article Snippet: Concentration was measured by Qubit RNA HS Assay on a Qubit fluorometer (ThermoFisher). .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

DNA Purification:

Standard Deviation:

Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
Article Snippet: One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems).

bioanalyzer 2100

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Related Articles

Methylation Sequencing:

DNA Extraction:

Amplification:

Electrophoresis:

Incubation:

Formalin-fixed Paraffin-Embedded:

Ex Vivo:

RNA Binding Assay:

Flow Cytometry:

Ligation:

Methylation:

Cell Culture:

Generated:

DNA HS Assay:

Sequencing:

Sonication:

Affinity Purification:

Binding Assay:

Multiplexing:

RNA Sequencing Assay:

RNA HS Assay:

Magnetic Beads:

Isolation:

Size-exclusion Chromatography:

Purification:

Polymerase Chain Reaction:

Polyacrylamide Gel Electrophoresis:

cDNA Library Assay:

Agarose Gel Electrophoresis:

Chromatin Immunoprecipitation:

Software:

Real-time Polymerase Chain Reaction:

Multiplex Assay:

Selection:

Sample Prep:

Next-Generation Sequencing:

Random Hexamer Labeling:

Spectrophotometry:

Concentration Assay:

DNA Purification:

Standard Deviation:

Staining:

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