2100 bioanalyzer instrument  (Agilent technologies)

 
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    Name:
    2100 Electrophoresis Bioanalyzer Instrument
    Description:

    Catalog Number:
    G2939AA
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    Score:
    85
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    Structured Review

    Agilent technologies 2100 bioanalyzer instrument
    Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent <t>2100</t> <t>Bioanalyzer.</t> The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.

    https://www.bioz.com/result/2100 bioanalyzer instrument/product/Agilent technologies
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    2100 bioanalyzer instrument - by Bioz Stars, 2019-10
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    Images

    1) Product Images from "Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations"

    Article Title: Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations

    Journal: Oncotarget

    doi: 10.18632/oncotarget.11796

    Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent 2100 Bioanalyzer. The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.
    Figure Legend Snippet: Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent 2100 Bioanalyzer. The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.

    Techniques Used: Mutagenesis, Electrophoresis, Polymerase Chain Reaction, Synthesized, Isolation, Amplification, CTL Assay, Negative Control, RNA Sequencing Assay

    2) Product Images from "Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes"

    Article Title: Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes

    Journal: Scientific Reports

    doi: 10.1038/srep41114

    Depletion of rRNA from RNA samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of DNAse-treated RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.
    Figure Legend Snippet: Depletion of rRNA from RNA samples isolated from dual species P. aeruginosa / S. aureus cultures. A total of 2 μg of DNAse-treated RNA, isolated form a dual species P. aeruginosa PAO1 and S. aureus ATCC6538 culture, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria) or Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( A ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( B ) MICROBExpress or ( C ) Ribo-Zero kits are shown. ( D ) Percent of rRNA contamination as reported by the Agilent Bioanalyzer 2100 Expert Software in RNA samples from single and dual species cultures of P. aeruginosa and/or S. aureus treated with the Ribo-Zero or MICROBExpress kits. Untreated input RNA (Total) or RNA processed via Ribo-Zero or MICROBExpress treatment was subjected to qPCR analysis of P. aeruginosa ( E , G ) or S. aureus ( F , H ) rRNA transcript abundance. ( E , F ) qPCR threshold cycle (Cq) for the indicated rRNA transcripts. ( G , H ) Copy numbers of P. aeruginosa or S. aureus 16S, 23 s, and 5S rRNA transcripts were calculated using respective qPCR standard curves. cDNA synthesis for the qPCR reactions was performed using 10 ng of indicated RNA samples as input. Experiments were repeated using two biological replicates. Error bars indicate standard deviation.

    Techniques Used: Isolation, Software, Real-time Polymerase Chain Reaction, Standard Deviation

    Quantitative and qualitative comparison of RNA recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using Qubit fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.
    Figure Legend Snippet: Quantitative and qualitative comparison of RNA recovered following rRNA depletion. A total of 4 μg of DNAse-treated RNA, isolated form 3-day-old P. aeruginosa PAO1 biofilms, was subjected to treatment with the Illumina Ribo-Zero rRNA Removal Kit (Bacteria), Ambion MICROBExpress™ Bacterial mRNA Enrichment Kit and the Life Technologies RiboMinus Transcriptome Isolation Kit, Bacteria. Following rRNA depletion and ethanol/acetate precipitation and resuspension in equal volumes of water, the RNA was assessed using Qubit fluorimetric quantitation with the Qubit RNA HS Assay Kit. Yields are reported as total RNA recovered ( A ) and as percentage of the input RNA ( B ). The RNA samples were also assessed using the Bioanalyzer RNA 6000 Pico kit. Representative electropherograms of ( C ) starting total RNA material and aliquots of the RNA samples that have been processed using the ( D ) MICROBExpress, ( E ) RiboMinus, or ( F ) Ribo-Zero kits are shown. Dashed lines indicate peaks corresponding to 16S and 23S RNA traces, which were detected in total RNA, MICROBExpress, and RiboMins samples. ( G ) The area of 16S and 23S rRNA peaks as percent of the total detected RNA was estimated, as determined using the 2100 Expert Software. RFU, relative fluorescence units. Experiments were repeated using three biological replicates.

    Techniques Used: Isolation, Quantitation Assay, RNA HS Assay, Software, Fluorescence

    3) Product Images from ""

    Article Title:

    Journal: The Journal of Biological Chemistry

    doi: 10.1074/jbc.M112.364851

    Loss of DosR has a profound effect on ribosome and ribosomal RNA stability. Cultures of M. smegmatis mc 2 155 wild-type and the Δ dosR mutant were grown at 37 °C to mid-exponential phase ( A ), normoxic stationary phase ( B ), or hypoxic stationary phase ( C ). Cells were harvested, lysed, and ribosomes were isolated by ultracentrifugation and fractionated through a linear sucrose gradient (15–40%). Then the A 254 and refraction were determined per fraction and plotted. D and E , for ribosomal RNA stability experiments, cultures were grown to hypoxic stationary phase at 37 °C in LB. RNA was purified using the TRIzol reagent and analyzed with RNA Nano 6000 chips on an Agilent 2100 bioanalyzer. Traces shown are the average of three independent experiments and were normalized to account for chip variability.
    Figure Legend Snippet: Loss of DosR has a profound effect on ribosome and ribosomal RNA stability. Cultures of M. smegmatis mc 2 155 wild-type and the Δ dosR mutant were grown at 37 °C to mid-exponential phase ( A ), normoxic stationary phase ( B ), or hypoxic stationary phase ( C ). Cells were harvested, lysed, and ribosomes were isolated by ultracentrifugation and fractionated through a linear sucrose gradient (15–40%). Then the A 254 and refraction were determined per fraction and plotted. D and E , for ribosomal RNA stability experiments, cultures were grown to hypoxic stationary phase at 37 °C in LB. RNA was purified using the TRIzol reagent and analyzed with RNA Nano 6000 chips on an Agilent 2100 bioanalyzer. Traces shown are the average of three independent experiments and were normalized to account for chip variability.

    Techniques Used: Mutagenesis, Isolation, Purification, Chromatin Immunoprecipitation

    Related Articles

    Multiplexing:

    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.

    Centrifugation:

    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: First, a centrifugation step of 16.000g for 10 min was performed to ensure efficient depletion of residual cells, cell debris, and genomic DNA. .. 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).

    Amplification:

    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: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: For PCR analysis, 1.5 μL of cDNA was incubated with 1.25 U of Taq polymerase (Roche Diagnostics), 20 pM primers (reverse primer in exon 24, forward primer in exon 22), and one-time SuperTaq PCR buffer (Enzyme Technologies, UK) and amplified for 30 cycles, each consisting of an incubation for 30 s at 94°C, 30 s at 60°C, and 30 s at 72°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.

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    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. .. Quantitative real time PCR (qRT-PCR) was conducted to measure relative abundance of the following genes in cDNA: IL-4 (Mm00445259 m1), IL-5 (Mm00439646 m1).

    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: 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: Persistent antigen at vaccination sites induces tumor-specific CD8+ T cell sequestration, dysfunction and deletion
    Article Snippet: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX) on d 6 and 21 after vaccination with gp100/IFA+covax or gp100/saline+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. .. Processing of bead-level data was by methods previously described.

    Synthesized:

    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).

    Picogreen Assay:

    Article Title: Oropharyngeal microbiome evaluation highlights Neisseria abundance in active celiac patients
    Article Snippet: The V4-V6 amplified regions of each sample were purified and quality-assessed using the 2100 Bioanalyzer Instrument (Agilent, Santa Clara, CA, USA). .. Thus, 2 sequencing runs were totally performed with the Illumina MiSeq System (PE 300 × 2).

    Cell Isolation:

    Article Title: The Impact of Self-Identified Race on Epidemiologic Studies of Gene Expression
    Article Snippet: Each clinical center followed a standardized protocol for the technical aspects of sample collection and CD4+ T cell isolation. .. 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.

    Quantitative RT-PCR:

    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: Beclin 1 and autophagy are required for the tumorigenicity of breast cancer stem-like/progenitor cells
    Article Snippet: Paragraph title: RT–qPCR analysis ... RNA quality was checked by capillary electrophoresis using the Bioanalyzer 2100 device (Agilent Technologies, Massy, France).

    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: Beclin 1 and autophagy are required for the tumorigenicity of breast cancer stem-like/progenitor cells
    Article Snippet: Total RNA was extracted using the TriZOL reagent, according to the manufacturer's instructions (Invitrogen). .. 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).

    Microarray:

    Article Title: PNPLA1 has a crucial role in skin barrier function by directing acylceramide biosynthesis
    Article Snippet: Paragraph title: Microarray ... The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

    Article Title: Gene Transcriptional and Metabolic Profile Changes in Mimetic Aging Mice Induced by D-Galactose
    Article Snippet: 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). .. Next, double- strand cDNA was synthesized using PrimeScript RT reagent Kit (TaKaRa BIO, Shiga, Japan), and then labeled with cyanine-3-CTP.

    Incubation:

    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: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: For PCR analysis, 1.5 μL of cDNA was incubated with 1.25 U of Taq polymerase (Roche Diagnostics), 20 pM primers (reverse primer in exon 24, forward primer in exon 22), and one-time SuperTaq PCR buffer (Enzyme Technologies, UK) and amplified for 30 cycles, each consisting of an incubation for 30 s at 94°C, 30 s at 60°C, and 30 s at 72°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.

    Article Title: Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking
    Article Snippet: Samples were incubated for 2 hr at 4°C with end-over-end agitation. .. The concentration and integrity of all samples was measured using an Agilent 2100 Bioanalyzer, following the ‘RNA Nano’ or ‘RNA Pico’ protocols, where appropriate.

    Expressing:

    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). .. Fluorescently labelled antisense RNA (cRNA targets) were synthesized with a Low Input QuickAmp Labeling Kit according to the manufacturer's protocol (Agilent Technologies).

    Article Title: The Impact of Self-Identified Race on Epidemiologic Studies of Gene Expression
    Article Snippet: Paragraph title: PERIPHERAL BLOOD CD4+ LYMPHOCYTE EXPRESSION PROFILING ... 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: Cytogenetic and Transcriptomic Analysis of Human Endometrial MSC Retaining Proliferative Activity after Sublethal Heat Shock
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    Article Title: Asthma Induction During Development and Adult Lung Function, Behavior and Brain Gene Expression
    Article Snippet: Paragraph title: Adult Lung Cytokine Gene Expression ... 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: 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). .. Previously described PCR primers for the BECN1 gene target were used.

    Article Title: Persistent antigen at vaccination sites induces tumor-specific CD8+ T cell sequestration, dysfunction and deletion
    Article Snippet: Paragraph title: Gene expression profiling ... 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.

    Derivative Assay:

    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).

    Hybridization:

    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.

    Article Title: Gene Transcriptional and Metabolic Profile Changes in Mimetic Aging Mice Induced by D-Galactose
    Article Snippet: 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). .. Next, double- strand cDNA was synthesized using PrimeScript RT reagent Kit (TaKaRa BIO, Shiga, Japan), and then labeled with cyanine-3-CTP.

    Flow Cytometry:

    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. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    Lab-on-a-Chip:

    Article Title: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: For PCR analysis, 1.5 μL of cDNA was incubated with 1.25 U of Taq polymerase (Roche Diagnostics), 20 pM primers (reverse primer in exon 24, forward primer in exon 22), and one-time SuperTaq PCR buffer (Enzyme Technologies, UK) and amplified for 30 cycles, each consisting of an incubation for 30 s at 94°C, 30 s at 60°C, and 30 s at 72°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. .. cDNA was generated in 20 μL reactions, using 1,000 ng of total RNA with random hexamer primers (Roche Diagnostics) and transcriptor reverse transcriptase (Roche Diagnostics) according to the manufacturer’s instructions. ddPCR was performed in duplicate as previously described on 0.5 μL of cDNA using a TaqMan assay spanning the exon 22–23 junction to detect the non-skipped fragment and an assay spanning the exon 22–24 junction to detect the skipped fragment (sequences are listed in ).

    Infection:

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    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.

    Generated:

    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.

    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. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    Polymerase Chain Reaction:

    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: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: For PCR analysis, 1.5 μL of cDNA was incubated with 1.25 U of Taq polymerase (Roche Diagnostics), 20 pM primers (reverse primer in exon 24, forward primer in exon 22), and one-time SuperTaq PCR buffer (Enzyme Technologies, UK) and amplified for 30 cycles, each consisting of an incubation for 30 s at 94°C, 30 s at 60°C, and 30 s at 72°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.

    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).

    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. .. Quantitative real time PCR (qRT-PCR) was conducted to measure relative abundance of the following genes in cDNA: IL-4 (Mm00445259 m1), IL-5 (Mm00439646 m1).

    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: 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