bioanalyzer 2100  (Agilent technologies)

 
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    • 99
    Name:
    2100 Electrophoresis Bioanalyzer Instrument
    Description:

    Catalog Number:
    G2939AA
    Price:
    None
    Score:
    85
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    Structured Review

    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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    bioanalyzer 2100 - by Bioz Stars, 2019-10
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    Images

    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

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

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

    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

    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.
    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

    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

    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

    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

    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

    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

    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

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    Centrifugation:

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    Amplification:

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    Synthesized:

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    Picogreen Assay:

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    Cell Isolation:

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    Quantitative RT-PCR:

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    Electrophoresis:

    Article Title: Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome
    Article Snippet: For the preparation of the library, the same amount in mass of each sample was quantified in equivalent amounts to approximately 10 μg each, and for each mixture of libraries of the V3 16S rDNA region they were fractionated by electrophoresis in 2% agarose gel. .. The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ].

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    Microarray:

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    Incubation:

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    Derivative Assay:

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    Hybridization:

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    Flow Cytometry:

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    Lab-on-a-Chip:

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    Infection:

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    Generated:

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    Polymerase Chain Reaction:

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    Article Snippet: RNA integrity and quality were checked using an Agilent Bioanalyzer 2100. .. RNA integrity and quality were checked using an Agilent Bioanalyzer 2100.

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: We prepared samples for Roche 454 sequencing using indexing barcodes-containing primers during the PCR step in BLESS ( ). .. We purified PCR products of size comprised between 300 and 800 nt in gel, and analyzed them on the 2100 Bioanalyzer (Agilent) prior to sequencing. .. For BLESS Illumina library preparation, we used the TruSeq DNA sample preparation kit v2 (Illumina) without DNA fragmentation and library size selection.

    Article Title: Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients
    Article Snippet: The first PCR reaction was performed with the 2.5 × 5 PRIME MasterMix (Eppendorf) using the following cycling conditions: 94 °C for 2 min, 94 °C for 40 s, 60 °C for 40 s and 65 °C for 40 s for 40 cycles, 65 °C for 10 min. DNA fragments were then analyzed on 2% agarose gel and purified through Agencourt AMPure XP Beads (Beckman Coulter, Brea, CA, USA). .. The V4-V6 amplified regions of each sample were purified and quality-assessed using the 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA, USA).

    Article Title: Beclin 1 and autophagy are required for the tumorigenicity of breast cancer stem-like/progenitor cells
    Article Snippet: RNA quality was checked by capillary electrophoresis using the Bioanalyzer 2100 device (Agilent Technologies, Massy, France). .. Quantitative real-time PCR was performed using 4 μl of 50-fold diluted cDNA in a final volume of 10 μl using the SsoFast EvaGreen supermix according to the manufacturer's instructions (Bio-Rad) in a CFX96 thermal cycler (Bio-Rad).

    DNA Sequencing:

    Article Title: Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome
    Article Snippet: Paragraph title: 4.6. Construction of the V3-16S rDNA Library and High-Throughput DNA Sequencing ... The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ].

    Sequencing:

    Article Title: In vivo expression technology and 5′ end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection
    Article Snippet: A total of 30 μM of 5′ RNA adapter (5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′), based on the Illumina adapter sequence, (Oligonucleotide sequences © 2007–2009 Illumina, Inc., all rights reserved) was ligated to the 5′ ends of the TAP+ and TAP− treated RNA samples using 20 U RNA Ligase 1 (NEB), 1X RNA Ligase 1 Buffer, 10% DMSO, 1 mM ATP (NEB) and 40 U rRNasin (Promega) in 20 μl DEPC- H2 O and incubated at 20°C for 6 h. Reactions were then loaded into Heavy Phase Lock Gel tubes (5 PRIME) with equal volume PCI, ethanol precipitated and reconstituted in DEPC-H2 O. Fragmentation of the 5′ ligated RNA samples was conducted using RNA fragmentation reagents (Ambion) following manufacturer's instructions with a fragmentation time of 4 min at 70°C. .. Reactions were ethanol precipitated, reconstituted in DEPC–H2 O and analyzed with an Agilent 2100 Bioanalyzer.

    Article Title: Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock
    Article Snippet: In this approach, mRNA was fragmented, cDNA was synthesized, end repaired, and ligated to unique sequencing adaptors to form cDNA libraries. .. Quality control of prepared libraries was made using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
    Article Snippet: Paragraph title: Small RNA isolation and Solexa HiSeq sequencing ... RNA integrity and quality were checked using an Agilent Bioanalyzer 2100.

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: We prepared samples for Roche 454 sequencing using indexing barcodes-containing primers during the PCR step in BLESS ( ). .. We purified PCR products of size comprised between 300 and 800 nt in gel, and analyzed them on the 2100 Bioanalyzer (Agilent) prior to sequencing. .. For BLESS Illumina library preparation, we used the TruSeq DNA sample preparation kit v2 (Illumina) without DNA fragmentation and library size selection.

    Article Title: Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients
    Article Snippet: Paragraph title: DNA extraction and 16S rRNA sequencing ... The V4-V6 amplified regions of each sample were purified and quality-assessed using the 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA, USA).

    Article Title: Palmitic Acid Induces Müller Cell Inflammation that is Potentiated by Co-treatment with Glucose
    Article Snippet: RNA sample quality was confirmed using the 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA). .. RNA sample quality was confirmed using the 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA).

    DNA Extraction:

    Article Title: Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia
    Article Snippet: The RNA Integrity Number (RIN) was determined by fractionating RNA samples on the 6000 Nano chip (Agilent Technologies) on the Agilent 2100 Bioanalyzer. .. DNA was isolated from approximately 10 mg dry homogenized tissue from specimens coming from the MSSM and Penn brain banks.

    Article Title: Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients
    Article Snippet: Paragraph title: DNA extraction and 16S rRNA sequencing ... The V4-V6 amplified regions of each sample were purified and quality-assessed using the 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA, USA).

    Sensitive Assay:

    Article Title: Epigenetic markers in circulating cell‐free DNA as prognostic markers for survival of castration‐resistant prostate cancer patients, et al. Epigenetic markers in circulating cell‐free DNA as prognostic markers for survival of castration‐resistant prostate cancer patients
    Article Snippet: The cfDNA was eluted in 27 μl of elution buffer. .. Size and yield of cfDNA was evaluated on a high sensitivity DNA chip of the Agilent 2100 Expert Bioanalyzer (Agilent Technologies Inc. Santa Clara, CA) and with the dsDNA High Sensitivity assay kit on a Qubit 3.0 fluorimeter (Thermo Fisher Scientific, Eugene, OR). .. 2.3 A total of 20 μl of cfDNA was used for the bisulphite modification using a commercially available kit (EZ DNA Methylation‐Lightning Kit, Zymo D5030, Zymo Research, Orange, CA).

    Magnetic Beads:

    Article Title: Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock
    Article Snippet: After that, mRNA was extracted from total RNA using magnetic beads (Sileks, Sileks, MO, USA). cDNA libraries were prepared using NEBNext® mRNA Library Prep Reagent Set for Illumina (New England Biolabs, Ipswich, MA, USA). .. Quality control of prepared libraries was made using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
    Article Snippet: Thereafter, contaminating DNA was removed by digestion with 5 U RQ1 RNase-free DNase I (Promega, Fitchburg, WI) in 100 μL of the manufacturer’s supplied buffer (1X final concentration) at 37°C for 30 min. Purified RNAs were again cleaned up using Agencourt RNAClean XP magnetic beads, as above, and eluted into 30 μL H2 O. .. The concentration and integrity of all samples was measured using an Agilent 2100 Bioanalyzer, following the ‘RNA Nano’ or ‘RNA Pico’ protocols, where appropriate.

    Isolation:

    Article Title: The Impact of Self-Identified Race on Epidemiologic Studies of Gene Expression
    Article Snippet: CD4+ lymphocytes were isolated using anti-CD4+ microbeads by positive column separation (Miltenyi Biotec, Auburn, CA) according to a previously published protocol [ ; ]. .. Analysis using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) confirmed average total RNA yields of 2 μg per collection, with no evidence of DNA contamination, minimal evidence of RNA degradation, and 28S:16S ratios of 2.0.

    Article Title: In vivo expression technology and 5′ end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection
    Article Snippet: Reactions were ethanol precipitated, reconstituted in DEPC–H2 O and analyzed with an Agilent 2100 Bioanalyzer. .. RNA libraries were then 3′ end dephosphorylated using 10 U T4 Polynucleotide Kinase (PNK) (NEB), minus ATP, with 1X PNK buffer and 20 U rRNasin (Promega) at 37°C for 3 h. A subsequent PCI and ethanol precipitation was performed to purify the libraries, which were then size selected on an 8% polyacrylamide 8 M urea gel.

    Article Title: Gene Transcriptional and Metabolic Profile Changes in Mimetic Aging Mice Induced by D-Galactose
    Article Snippet: Total RNA was extracted from the frozen liver using the mirVanaTM RNA Isolation Kit (Applied Biosystems, Darmstadt, Germany) and then cleaned with Qiagen RNeasyMini kit (Qiagen, Chatsworth, CA), according to the manufacturer’s instructions. .. The total RNA was quantified using NanoDrop ND-2000 (Thermo Scientific, Wilmington, DE) and the RNA integrity was evaluated using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

    Article Title: Deciphering genetic regulation of CD14 by SP1 through characterization of peripheral blood mononuclear transcriptome of P. faiciparum and P. vivax infected malaria patients
    Article Snippet: Total RNA was isolated following manufacturer's protocol using RNeasy® Plus Minikit (QIAGEN) and quantified using nanodrop 2000C spectrophotometer (Thermo Scientific). .. Integrity values were checked using Agilent 2100 Bioanalyzer instrument.

    Article Title: A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains
    Article Snippet: Paragraph title: Isolation of peripheral blood mononuclear cells and RNA extraction ... RNA amounts and purity were measured with Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

    Article Title: High-throughput sequencing of two populations of extracellular vesicles provides an mRNA signature that can be detected in the circulation of breast cancer patients
    Article Snippet: Paragraph title: RNA isolation and profiling ... The quality of RNA was assessed by total RNA electropherogram profile, using an Agilent 2100 bioanalyzer (Total RNA Nano Series II).

    Article Title: The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
    Article Snippet: Paragraph title: Small RNA isolation and Solexa HiSeq sequencing ... RNA integrity and quality were checked using an Agilent Bioanalyzer 2100.

    Article Title: Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia
    Article Snippet: Total RNA was isolated from approximately 50 mg homogenized tissue in Trizol using the RNeasy kit according to manufacturer protocol. .. The RNA Integrity Number (RIN) was determined by fractionating RNA samples on the 6000 Nano chip (Agilent Technologies) on the Agilent 2100 Bioanalyzer.

    Article Title: Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
    Article Snippet: Paragraph title: APEX-RIP, Part II: Cell lysis, streptavidin bead enrichment of biotinylated material and RNA isolation ... The concentration and integrity of all samples was measured using an Agilent 2100 Bioanalyzer, following the ‘RNA Nano’ or ‘RNA Pico’ protocols, where appropriate.

    Article Title: Palmitic Acid Induces Müller Cell Inflammation that is Potentiated by Co-treatment with Glucose
    Article Snippet: Paragraph title: RNA isolation, RNAseq, and analysis ... RNA sample quality was confirmed using the 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA).

    Multiplex Assay:

    Article Title: Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock
    Article Snippet: Dual indexing was performed by PCR with NEBNext Multiplex Oligos for Illumina (dual index primers set 1). .. Quality control of prepared libraries was made using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Labeling:

    Article Title: The Impact of Self-Identified Race on Epidemiologic Studies of Gene Expression
    Article Snippet: Analysis using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) confirmed average total RNA yields of 2 μg per collection, with no evidence of DNA contamination, minimal evidence of RNA degradation, and 28S:16S ratios of 2.0. .. Analysis using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) confirmed average total RNA yields of 2 μg per collection, with no evidence of DNA contamination, minimal evidence of RNA degradation, and 28S:16S ratios of 2.0.

    Purification:

    Article Title: PNPLA1 has a crucial role in skin barrier function by directing acylceramide biosynthesis
    Article Snippet: Total RNA extracted from P0 newborns was purified using a RNeasy Mini Kit (QIAGEN). .. The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

    Article Title: Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome
    Article Snippet: The amplicon was cut from the gel and purified using the SV PCR Cleaning System and the system (Promega, Madison, WI, USA). .. The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ].

    Article Title: In vivo expression technology and 5′ end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection
    Article Snippet: Reactions were ethanol precipitated, reconstituted in DEPC–H2 O and analyzed with an Agilent 2100 Bioanalyzer. .. Reactions were ethanol precipitated, reconstituted in DEPC–H2 O and analyzed with an Agilent 2100 Bioanalyzer.

    Article Title: A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains
    Article Snippet: Total RNA was isolated and purified with RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. .. RNA amounts and purity were measured with Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

    Article Title: The small RNA diversity from Medicago truncatula roots under biotic interactions evidences the environmental plasticity of the miRNAome
    Article Snippet: RNA integrity and quality were checked using an Agilent Bioanalyzer 2100. .. RNA integrity and quality were checked using an Agilent Bioanalyzer 2100.

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: We prepared samples for Roche 454 sequencing using indexing barcodes-containing primers during the PCR step in BLESS ( ). .. We purified PCR products of size comprised between 300 and 800 nt in gel, and analyzed them on the 2100 Bioanalyzer (Agilent) prior to sequencing. .. For BLESS Illumina library preparation, we used the TruSeq DNA sample preparation kit v2 (Illumina) without DNA fragmentation and library size selection.

    Article Title: Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
    Article Snippet: Thereafter, contaminating DNA was removed by digestion with 5 U RQ1 RNase-free DNase I (Promega, Fitchburg, WI) in 100 μL of the manufacturer’s supplied buffer (1X final concentration) at 37°C for 30 min. Purified RNAs were again cleaned up using Agencourt RNAClean XP magnetic beads, as above, and eluted into 30 μL H2 O. .. The concentration and integrity of all samples was measured using an Agilent 2100 Bioanalyzer, following the ‘RNA Nano’ or ‘RNA Pico’ protocols, where appropriate.

    Article Title: Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients
    Article Snippet: The Illumina indices were inserted on each amplified region according to the Nextera XT protocol (Illumina, San Diego, CA, USA). .. The V4-V6 amplified regions of each sample were purified and quality-assessed using the 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA, USA). .. Library quantification was performed using the Qubit dsDNA BR assay kit (Life Technologies, CA, USA).

    Article Title: Palmitic Acid Induces Müller Cell Inflammation that is Potentiated by Co-treatment with Glucose
    Article Snippet: Treated cells were lysed and RNA purified using the RNeasy mini kit (Qiagen; Valencia, CA) according to the manufacturer’s protocol. .. RNA sample quality was confirmed using the 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA).

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: Paragraph title: RT-PCR ... Exon-skipping levels were semiquantitatively determined as the percentages of the total (wild-type and skipped) product with the Agilent 2100 Bioanalyzer (lab-on-a-chip analyzer) as described previously by Spitali et al.

    Article Title: Asthma Induction During Development and Adult Lung Function, Behavior and Brain Gene Expression
    Article Snippet: RNA quantity and quality were determined with a NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 BioAnalyzer™ (Agilent Technologies, Santa Clara, CA, USA), respectively. .. We also conducted PCR to measure IL-13 expression (Mm00434204 m1), but because of poor amplification, we do not report these results here.

    Lysis:

    Article Title: Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
    Article Snippet: Paragraph title: APEX-RIP, Part II: Cell lysis, streptavidin bead enrichment of biotinylated material and RNA isolation ... The concentration and integrity of all samples was measured using an Agilent 2100 Bioanalyzer, following the ‘RNA Nano’ or ‘RNA Pico’ protocols, where appropriate.

    cDNA Library Assay:

    Article Title: In vivo expression technology and 5′ end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection
    Article Snippet: Paragraph title: cDNA library preparations ... Reactions were ethanol precipitated, reconstituted in DEPC–H2 O and analyzed with an Agilent 2100 Bioanalyzer.

    Agarose Gel Electrophoresis:

    Article Title: Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome
    Article Snippet: For the preparation of the library, the same amount in mass of each sample was quantified in equivalent amounts to approximately 10 μg each, and for each mixture of libraries of the V3 16S rDNA region they were fractionated by electrophoresis in 2% agarose gel. .. The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ].

    Article Title: Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients
    Article Snippet: The first PCR reaction was performed with the 2.5 × 5 PRIME MasterMix (Eppendorf) using the following cycling conditions: 94 °C for 2 min, 94 °C for 40 s, 60 °C for 40 s and 65 °C for 40 s for 40 cycles, 65 °C for 10 min. DNA fragments were then analyzed on 2% agarose gel and purified through Agencourt AMPure XP Beads (Beckman Coulter, Brea, CA, USA). .. The V4-V6 amplified regions of each sample were purified and quality-assessed using the 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA, USA).

    Mouse Assay:

    Article Title: Persistent antigen at vaccination sites induces tumor-specific CD8+ T cell sequestration, dysfunction and deletion
    Article Snippet: Mice received 1, 000 pmel-1 T cells i.v. and s.c. vaccination with gp100/saline or gp100/IFA followed by covax. .. After confirmation of RNA quality using a Bioanalyzer 2100 instrument (Agilent), 100 ng or less of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA Amplification kits (Ambion), and hybridized to Illumina Ref-6 version 2 mouse whole-genome arrays.

    Chromatin Immunoprecipitation:

    Article Title: The Impact of Self-Identified Race on Epidemiologic Studies of Gene Expression
    Article Snippet: Analysis using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) confirmed average total RNA yields of 2 μg per collection, with no evidence of DNA contamination, minimal evidence of RNA degradation, and 28S:16S ratios of 2.0. .. Labeled cRNA was combined with formamide and hybridization buffer, followed by overnight hybridization to HumanRef8Bead-Chip arrays.

    Article Title: Gene Expression Elucidates Functional Impact of Polygenic Risk for Schizophrenia
    Article Snippet: The mean total RNA yield was 15.3 ug (+/− 5.7). .. The RNA Integrity Number (RIN) was determined by fractionating RNA samples on the 6000 Nano chip (Agilent Technologies) on the Agilent 2100 Bioanalyzer. .. 51 samples with RIN < 5.5 were excluded from the study (see Sample QC below).

    Article Title: Epigenetic markers in circulating cell‐free DNA as prognostic markers for survival of castration‐resistant prostate cancer patients, et al. Epigenetic markers in circulating cell‐free DNA as prognostic markers for survival of castration‐resistant prostate cancer patients
    Article Snippet: The cfDNA was eluted in 27 μl of elution buffer. .. Size and yield of cfDNA was evaluated on a high sensitivity DNA chip of the Agilent 2100 Expert Bioanalyzer (Agilent Technologies Inc. Santa Clara, CA) and with the dsDNA High Sensitivity assay kit on a Qubit 3.0 fluorimeter (Thermo Fisher Scientific, Eugene, OR). .. 2.3 A total of 20 μl of cfDNA was used for the bisulphite modification using a commercially available kit (EZ DNA Methylation‐Lightning Kit, Zymo D5030, Zymo Research, Orange, CA).

    Software:

    Article Title: PNPLA1 has a crucial role in skin barrier function by directing acylceramide biosynthesis
    Article Snippet: The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies). .. Samples were hybridized to the Mouse Gene Expression 4x44K v2 Microarray (G4846A, Agilent Technologies), washed, and then scanned using a SureScan Microarray Scanner (Agilent Technologies).

    Article Title: Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome
    Article Snippet: The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ]. .. The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ].

    Article Title: Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock
    Article Snippet: Quality control of prepared libraries was made using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). .. Next-generation sequencing was done by parallel measurement of three biological samples, both for control and SHS-treated eMSC.

    Article Title: Persistent antigen at vaccination sites induces tumor-specific CD8+ T cell sequestration, dysfunction and deletion
    Article Snippet: After confirmation of RNA quality using a Bioanalyzer 2100 instrument (Agilent), 100 ng or less of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA Amplification kits (Ambion), and hybridized to Illumina Ref-6 version 2 mouse whole-genome arrays. .. After confirmation of RNA quality using a Bioanalyzer 2100 instrument (Agilent), 100 ng or less of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA Amplification kits (Ambion), and hybridized to Illumina Ref-6 version 2 mouse whole-genome arrays.

    Real-time Polymerase Chain Reaction:

    Article Title: Asthma Induction During Development and Adult Lung Function, Behavior and Brain Gene Expression
    Article Snippet: RNA quantity and quality were determined with a NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 BioAnalyzer™ (Agilent Technologies, Santa Clara, CA, USA), respectively. .. RNA quantity and quality were determined with a NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 BioAnalyzer™ (Agilent Technologies, Santa Clara, CA, USA), respectively.

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: We purified PCR products of size comprised between 300 and 800 nt in gel, and analyzed them on the 2100 Bioanalyzer (Agilent) prior to sequencing. .. For gDNA sequencing, we sheared gDNA with Covaris S220 AFA (Covaris) according to the manufacturer’s instructions prior to Illumina library preparation.

    Article Title: Beclin 1 and autophagy are required for the tumorigenicity of breast cancer stem-like/progenitor cells
    Article Snippet: RNA quality was checked by capillary electrophoresis using the Bioanalyzer 2100 device (Agilent Technologies, Massy, France). .. One microgram of total RNA was reverse-transcribed using oligo(dT) and random hexamer primers, using the iScript cDNA synthesis kit according to the manufacturer's recommendations (Bio-Rad).

    RNA Extraction:

    Article Title: Asthma Induction During Development and Adult Lung Function, Behavior and Brain Gene Expression
    Article Snippet: Tissue RNA extraction was conducted using TRIzol reagent (Invitrogen; Carlsbad, CA, USA) and Qiagen RNeasy columns (Qiagen, Germantown, MD, USA). .. RNA quantity and quality were determined with a NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 BioAnalyzer™ (Agilent Technologies, Santa Clara, CA, USA), respectively.

    Article Title: A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains
    Article Snippet: Paragraph title: Isolation of peripheral blood mononuclear cells and RNA extraction ... RNA amounts and purity were measured with Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

    Sample Prep:

    Article Title: Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock
    Article Snippet: Sample preparation for NGS and sequencing on the Illumina platform were performed in Genotek company (Moscow, Russia). .. Quality control of prepared libraries was made using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Palmitic Acid Induces Müller Cell Inflammation that is Potentiated by Co-treatment with Glucose
    Article Snippet: RNA sample quality was confirmed using the 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA). .. RNA sample quality was confirmed using the 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA).

    Ethanol Precipitation:

    Article Title: High-throughput sequencing of two populations of extracellular vesicles provides an mRNA signature that can be detected in the circulation of breast cancer patients
    Article Snippet: Total RNA was extracted from U87 cells and derived large oncosome (LO) and nano-sized EV (Exo) fractions, as well as from plasma EVs by ethanol precipitation. .. The quality of RNA was assessed by total RNA electropherogram profile, using an Agilent 2100 bioanalyzer (Total RNA Nano Series II).

    Next-Generation Sequencing:

    Article Title: Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock
    Article Snippet: Paragraph title: 2.8. mRNA Expression Analysis by Next-Generation Sequencing ... Quality control of prepared libraries was made using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: Paragraph title: Next-generation sequencing ... We purified PCR products of size comprised between 300 and 800 nt in gel, and analyzed them on the 2100 Bioanalyzer (Agilent) prior to sequencing.

    Random Hexamer Labeling:

    Article Title: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: cDNA was generated using 400 ng of RNA in a 20 μL reaction with random hexamer primers and transcriptor reverse transcriptase (Roche Diagnostics) for 45 min at 42°C. .. Exon-skipping levels were semiquantitatively determined as the percentages of the total (wild-type and skipped) product with the Agilent 2100 Bioanalyzer (lab-on-a-chip analyzer) as described previously by Spitali et al.

    Spectrophotometry:

    Article Title: Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome
    Article Snippet: The DNA concentration of each library was measured by a NanoDrop Lite spectrophotometer (Thermo Scientific). .. The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ].

    Article Title: Deciphering genetic regulation of CD14 by SP1 through characterization of peripheral blood mononuclear transcriptome of P. faiciparum and P. vivax infected malaria patients
    Article Snippet: Total RNA was isolated following manufacturer's protocol using RNeasy® Plus Minikit (QIAGEN) and quantified using nanodrop 2000C spectrophotometer (Thermo Scientific). .. Integrity values were checked using Agilent 2100 Bioanalyzer instrument.

    Article Title: Asthma Induction During Development and Adult Lung Function, Behavior and Brain Gene Expression
    Article Snippet: Tissue RNA extraction was conducted using TRIzol reagent (Invitrogen; Carlsbad, CA, USA) and Qiagen RNeasy columns (Qiagen, Germantown, MD, USA). .. RNA quantity and quality were determined with a NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 BioAnalyzer™ (Agilent Technologies, Santa Clara, CA, USA), respectively. .. Complementary DNA (cDNA) was reverse transcribed from RNA with High-Capacity cDNA Reverse Transcription kits (Applied Biosystems, Wilmington, DE, USA).

    Concentration Assay:

    Article Title: Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome
    Article Snippet: The DNA concentration of each library was measured by a NanoDrop Lite spectrophotometer (Thermo Scientific). .. The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ]. .. We performed the sequencing using the Ion 316 Chip Kit v2 (Carlsbad, CA, USA) and the Ion Torrent PGM System (Guilford, CT, USA.).

    Article Title: Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
    Article Snippet: Thereafter, contaminating DNA was removed by digestion with 5 U RQ1 RNase-free DNase I (Promega, Fitchburg, WI) in 100 μL of the manufacturer’s supplied buffer (1X final concentration) at 37°C for 30 min. Purified RNAs were again cleaned up using Agencourt RNAClean XP magnetic beads, as above, and eluted into 30 μL H2 O. .. The concentration and integrity of all samples was measured using an Agilent 2100 Bioanalyzer, following the ‘RNA Nano’ or ‘RNA Pico’ protocols, where appropriate. .. Samples were not heat-cooled prior to loading Bioanalyzer chips.

    High Throughput Screening Assay:

    Article Title: Gut Microbiota and Predicted Metabolic Pathways in a Sample of Mexican Women Affected by Obesity and Obesity Plus Metabolic Syndrome
    Article Snippet: Paragraph title: 4.6. Construction of the V3-16S rDNA Library and High-Throughput DNA Sequencing ... The concentration and average size of each amplicon of the library were calculated with an Agilent 2100 bioanalyzer as previously described [ ].

    FACS:

    Article Title: Persistent antigen at vaccination sites induces tumor-specific CD8+ T cell sequestration, dysfunction and deletion
    Article Snippet: Six and 21 d later, Splenocyte suspensions were RBC-lysed 6 and 21 d later and pmel-1 T cells were column-sorted using magnetic microbeads (Miltenyi Biotech) coated with CD90.1 mAb, followed by FACS-sorting using CD8 and CD90.1. .. After confirmation of RNA quality using a Bioanalyzer 2100 instrument (Agilent), 100 ng or less of total RNA was amplified and biotin-labeled through a two-round Eberwine procedure using MessageAmp II and Illumina TotalPrep RNA Amplification kits (Ambion), and hybridized to Illumina Ref-6 version 2 mouse whole-genome arrays.

    Gradient Centrifugation:

    Article Title: Deciphering genetic regulation of CD14 by SP1 through characterization of peripheral blood mononuclear transcriptome of P. faiciparum and P. vivax infected malaria patients
    Article Snippet: 2.2 Immediately after drawing blood, PBMC were separated from venous blood of 44 patients (P. falciparum infected = 28; P. vivax infected = 12 and P. falciparum convalescence = 4) using Histopaque 1077 (Sigma Aldrich, St. Louis, MO) and density gradient centrifugation according to manufacturer's protocol. .. Integrity values were checked using Agilent 2100 Bioanalyzer instrument.

    Article Title: A new high-throughput sequencing method for determining diversity and similarity of T cell receptor (TCR) α and β repertoires and identifying potential new invariant TCR α chains
    Article Snippet: Peripheral blood mononuclear cells (PBMCs) were isolated with Ficoll-Paque PLUS™ (GE Healthcare Health Sciences, Uppsala, Sweden) density gradient centrifugation and washed with phosphate buffered saline (PBS). .. RNA amounts and purity were measured with Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

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    Agilent technologies 2100 bioanalyzer
    Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent <t>2100</t> <t>Bioanalyzer)</t> of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated
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    Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of fixation and postfixation processing on total cellular RNA: gel-simulated image (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Lane L: RNA ladder. Lane 1: Native non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of fixation and postfixation processing on total cellular RNA: gel-simulated image (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Lane L: RNA ladder. Lane 1: Native non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of buffer composition on postfixation processing of an RNA 50mer: gel-simulated image (Agilent 2100 Bioanalyzer). Lane L: RNA ladder. Lane 1: Native RNA 50mer. Lane 2: RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Excess formaldehyde

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of buffer composition on postfixation processing of an RNA 50mer: gel-simulated image (Agilent 2100 Bioanalyzer). Lane L: RNA ladder. Lane 1: Native RNA 50mer. Lane 2: RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. Excess formaldehyde

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Postformaldehyde fixation processing of an RNA 50mer. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours and then heated at 70°C for 30 minutes, where indicated, in the following

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Postformaldehyde fixation processing of an RNA 50mer. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours and then heated at 70°C for 30 minutes, where indicated, in the following

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques:

    Effects of fixation and postfixation processing on total HeLa RNA. Electropherograms (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. FU denotes fluorescence units. A: Non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

    Figure Lengend Snippet: Effects of fixation and postfixation processing on total HeLa RNA. Electropherograms (Agilent 2100 Bioanalyzer) of total cellular RNA fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. FU denotes fluorescence units. A: Non–formaldehyde-treated

    Article Snippet: The compositions of the total HeLa RNA and RNA 50mer preparations were characterized by capillary electrophoresis using a 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

    Techniques: Fluorescence

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

    Article Snippet: The Agilent 2100 Expert software analyze DNA profile of each sample automatically and displays electropherogram for each sample.

    Techniques:

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

    Article Snippet: The Agilent 2100 Expert software analyze DNA profile of each sample automatically and displays electropherogram for each sample.

    Techniques:

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

    Article Snippet: The Agilent 2100 Expert software analyze DNA profile of each sample automatically and displays electropherogram for each sample.

    Techniques:

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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-018-5096-9

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

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

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

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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-018-5096-9

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

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

    Techniques: Formalin-fixed Paraffin-Embedded, Positive Control

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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-018-5096-9

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

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

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