bioanalyzer  (Agilent technologies)

 
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    Bioanalyzer chips and reagents
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    Structured Review

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

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    Images

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

    Article Title: Unlocking Short Read Sequencing for Metagenomics

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0011840

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

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

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

    Techniques Used: Isolation, Concentration Assay, Purification

    2) Product Images from "Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples"

    Article Title: Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples

    Journal: Scientific Reports

    doi: 10.1038/srep34850

    Bioanalyzer analysis of total RNA and bacterial mRNA-enriched samples from Drosophila ananassae colonized by its Wolbachia endosymbiont. The subtraction of Drosophila rRNA was assessed by running equivalent amounts of total RNA ( blue ) and Ribo-Zero reduced RNA ( pink ) on a Bioanalyzer. The software calculated the concentration of each sample by integrating the area under the rRNA peaks. Total RNA was 331 ng/μL and Ribo-Zero reduced RNA was 8 ng/μL, for an RNA loss of > 97%, most of which is in the rRNA peaks for both the bacterial endosymbiont and invertebrate host.
    Figure Legend Snippet: Bioanalyzer analysis of total RNA and bacterial mRNA-enriched samples from Drosophila ananassae colonized by its Wolbachia endosymbiont. The subtraction of Drosophila rRNA was assessed by running equivalent amounts of total RNA ( blue ) and Ribo-Zero reduced RNA ( pink ) on a Bioanalyzer. The software calculated the concentration of each sample by integrating the area under the rRNA peaks. Total RNA was 331 ng/μL and Ribo-Zero reduced RNA was 8 ng/μL, for an RNA loss of > 97%, most of which is in the rRNA peaks for both the bacterial endosymbiont and invertebrate host.

    Techniques Used: Software, Concentration Assay

    Bioanalyzer analysis of Ehrlichia and canine total RNA abundance. Using the Bioanalyzer, the Ehrlichia- canine total RNA (blue, left axis) was compared to the RNA 6000 ladder (pink, right axis), which contains 0.2, 0.5, 1.0, 2.0, 4.0, and 6.0 kbp fragments. Only canine rRNA was evident with no detectable bacterial rRNAs.
    Figure Legend Snippet: Bioanalyzer analysis of Ehrlichia and canine total RNA abundance. Using the Bioanalyzer, the Ehrlichia- canine total RNA (blue, left axis) was compared to the RNA 6000 ladder (pink, right axis), which contains 0.2, 0.5, 1.0, 2.0, 4.0, and 6.0 kbp fragments. Only canine rRNA was evident with no detectable bacterial rRNAs.

    Techniques Used:

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

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

    Journal: Scientific Reports

    doi: 10.1038/srep37137

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

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

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

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

    4) Product Images from "Molecular strain typing of the yaws pathogen, Treponema pallidum subspecies pertenue"

    Article Title: Molecular strain typing of the yaws pathogen, Treponema pallidum subspecies pertenue

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0203632

    RFLP patterns of T . pallidum subsp. pertenue . (A) The tpr E , G , and J genes were amplified in a nested PCR to produce a mixed amplicon approximately 1830–1848 bp in length. Following PCR, amplicons were digested with the enzyme Mse I and analyzed on an Agilent Bioanalyzer. Two RFLP patterns ( q and r ) were observed among the clinical specimens and laboratory strains analyzed, including those for strains only partially typed (data not shown). The sizes of each fragment were confirmed through sequencing and are indicated in red. The Nichols TPA strain was used as a control for RFLP. The violet and green bands visible in each lane depict the Bioanalyzer kit’s internal control upper and lower bands, respectively. (B) Each of the tpr E , G , and J genes was amplified directly from the genome and sequenced. Regions of the products between the IP6 and IP7 primer annealing sequences were analyzed for Mse I restriction sites for both patterns. Approximate positions of each site (indicated as “M”) are shown. Sizes between each restriction site are listed in red.
    Figure Legend Snippet: RFLP patterns of T . pallidum subsp. pertenue . (A) The tpr E , G , and J genes were amplified in a nested PCR to produce a mixed amplicon approximately 1830–1848 bp in length. Following PCR, amplicons were digested with the enzyme Mse I and analyzed on an Agilent Bioanalyzer. Two RFLP patterns ( q and r ) were observed among the clinical specimens and laboratory strains analyzed, including those for strains only partially typed (data not shown). The sizes of each fragment were confirmed through sequencing and are indicated in red. The Nichols TPA strain was used as a control for RFLP. The violet and green bands visible in each lane depict the Bioanalyzer kit’s internal control upper and lower bands, respectively. (B) Each of the tpr E , G , and J genes was amplified directly from the genome and sequenced. Regions of the products between the IP6 and IP7 primer annealing sequences were analyzed for Mse I restriction sites for both patterns. Approximate positions of each site (indicated as “M”) are shown. Sizes between each restriction site are listed in red.

    Techniques Used: Amplification, Nested PCR, Polymerase Chain Reaction, Sequencing

    Analysis of the arp 60-bp repeat region. (A) A portion of the arp gene was amplified through PCR and run on an Agilent Bioanalyzer for each sample. Seven patterns containing 2, 3, 4, 5, 6, 9, and 10 repeats were identified among the samples tested in the lab, and an additional pattern (12 repeats) was seen following in silico analysis of one of the published genomes (not shown). The Nichols TPA strain, which contains 14 repeats, was used as a reference. The violet and green bands visible in each lane depict the Bioanalyzer kit’s internal control upper and lower bands, respectively. (B) Distribution of repeat sizes in clinical specimens from Vanuatu, Ghana clinical specimens, and among laboratory strains.
    Figure Legend Snippet: Analysis of the arp 60-bp repeat region. (A) A portion of the arp gene was amplified through PCR and run on an Agilent Bioanalyzer for each sample. Seven patterns containing 2, 3, 4, 5, 6, 9, and 10 repeats were identified among the samples tested in the lab, and an additional pattern (12 repeats) was seen following in silico analysis of one of the published genomes (not shown). The Nichols TPA strain, which contains 14 repeats, was used as a reference. The violet and green bands visible in each lane depict the Bioanalyzer kit’s internal control upper and lower bands, respectively. (B) Distribution of repeat sizes in clinical specimens from Vanuatu, Ghana clinical specimens, and among laboratory strains.

    Techniques Used: Amplification, Polymerase Chain Reaction, In Silico

    5) Product Images from "Comparing DNA quantity and quality using saliva collection following food and beverage consumption"

    Article Title: Comparing DNA quantity and quality using saliva collection following food and beverage consumption

    Journal: BMC Research Notes

    doi: 10.1186/s13104-019-4211-6

    Bioanalyzer electropherogram traces of the spit samples. Each subject is shown individually with colors representing collection conditions: following manufacturer’s instructions (red), after consuming water (blue), after eating lunch (green), after consuming a carbonated beverage (cyan), after consuming a sports drink (magenta), and after consuming coffee (orange)
    Figure Legend Snippet: Bioanalyzer electropherogram traces of the spit samples. Each subject is shown individually with colors representing collection conditions: following manufacturer’s instructions (red), after consuming water (blue), after eating lunch (green), after consuming a carbonated beverage (cyan), after consuming a sports drink (magenta), and after consuming coffee (orange)

    Techniques Used:

    Sample concentrations by three different methods of quantification (Nanodrop, Qubit, and Bioanalyzer) and a purity assessment by the ratio of absorbance at 260 and 280 nm. “CatchAll” conditions are the two swab collections and “Genefix” are the six spit collections. Swab sample concentrations are plotted on the left y-axis while spit sample concentrations are plotted on the right y-axis. Two axes were used as the swab sample without secondary purification (CatchAll + QuickExtract) contains contaminants that absorb at 260 nm in the Nanodrop. *p
    Figure Legend Snippet: Sample concentrations by three different methods of quantification (Nanodrop, Qubit, and Bioanalyzer) and a purity assessment by the ratio of absorbance at 260 and 280 nm. “CatchAll” conditions are the two swab collections and “Genefix” are the six spit collections. Swab sample concentrations are plotted on the left y-axis while spit sample concentrations are plotted on the right y-axis. Two axes were used as the swab sample without secondary purification (CatchAll + QuickExtract) contains contaminants that absorb at 260 nm in the Nanodrop. *p

    Techniques Used: Purification

    6) Product Images from "An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer"

    Article Title: An Improved Breast Epithelial Sampling Method for Molecular Profiling and Biomarker Analysis in Women at Risk for Breast Cancer

    Journal: Breast Cancer : Basic and Clinical Research

    doi: 10.4137/BCBCR.S23577

    Electropherogram of RNA from ductal epithelial samples . Total RNA was extracted from ductal lavage samples and examined by Agilent 2100 Bioanalyzer nanoassay. Electropherograms for RNA extracted from a frozen pellet without RNAlater treatment ( A ) or from a frozen pellet treated with RNAlater ( B ) are depicted. FU, fluorescence units. The peak at 25 nt is an internal standard.
    Figure Legend Snippet: Electropherogram of RNA from ductal epithelial samples . Total RNA was extracted from ductal lavage samples and examined by Agilent 2100 Bioanalyzer nanoassay. Electropherograms for RNA extracted from a frozen pellet without RNAlater treatment ( A ) or from a frozen pellet treated with RNAlater ( B ) are depicted. FU, fluorescence units. The peak at 25 nt is an internal standard.

    Techniques Used: Fluorescence

    Gel electrophoresis of DNA and RNA samples . Agarose gel electrophoresis of intact genomic DNA from the indicated ductal lavage samples ( A ). Lane 1 indicates separation of 100-bp markers. Bioanalyzer gel electrophoresis of total RNA from the indicated ductal lavage samples ( B ).
    Figure Legend Snippet: Gel electrophoresis of DNA and RNA samples . Agarose gel electrophoresis of intact genomic DNA from the indicated ductal lavage samples ( A ). Lane 1 indicates separation of 100-bp markers. Bioanalyzer gel electrophoresis of total RNA from the indicated ductal lavage samples ( B ).

    Techniques Used: Nucleic Acid Electrophoresis, Agarose Gel Electrophoresis, Electrophoresis

    7) Product Images from "Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples"

    Article Title: Efficient Enrichment of Bacterial mRNA from Host-Bacteria Total RNA Samples

    Journal: Scientific Reports

    doi: 10.1038/srep34850

    Bioanalyzer analysis of total RNA and bacterial mRNA-enriched samples from Drosophila ananassae colonized by its Wolbachia endosymbiont. The subtraction of Drosophila rRNA was assessed by running equivalent amounts of total RNA ( blue ) and Ribo-Zero reduced RNA ( pink ) on a Bioanalyzer. The software calculated the concentration of each sample by integrating the area under the rRNA peaks. Total RNA was 331 ng/μL and Ribo-Zero reduced RNA was 8 ng/μL, for an RNA loss of > 97%, most of which is in the rRNA peaks for both the bacterial endosymbiont and invertebrate host.
    Figure Legend Snippet: Bioanalyzer analysis of total RNA and bacterial mRNA-enriched samples from Drosophila ananassae colonized by its Wolbachia endosymbiont. The subtraction of Drosophila rRNA was assessed by running equivalent amounts of total RNA ( blue ) and Ribo-Zero reduced RNA ( pink ) on a Bioanalyzer. The software calculated the concentration of each sample by integrating the area under the rRNA peaks. Total RNA was 331 ng/μL and Ribo-Zero reduced RNA was 8 ng/μL, for an RNA loss of > 97%, most of which is in the rRNA peaks for both the bacterial endosymbiont and invertebrate host.

    Techniques Used: Software, Concentration Assay

    Bioanalyzer analysis of Ehrlichia and canine total RNA abundance. Using the Bioanalyzer, the Ehrlichia- canine total RNA (blue, left axis) was compared to the RNA 6000 ladder (pink, right axis), which contains 0.2, 0.5, 1.0, 2.0, 4.0, and 6.0 kbp fragments. Only canine rRNA was evident with no detectable bacterial rRNAs.
    Figure Legend Snippet: Bioanalyzer analysis of Ehrlichia and canine total RNA abundance. Using the Bioanalyzer, the Ehrlichia- canine total RNA (blue, left axis) was compared to the RNA 6000 ladder (pink, right axis), which contains 0.2, 0.5, 1.0, 2.0, 4.0, and 6.0 kbp fragments. Only canine rRNA was evident with no detectable bacterial rRNAs.

    Techniques Used:

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

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

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0127146

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

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

    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 "RNA sequencing data of Notch ligand treated human dental pulp cells"

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

    Journal: Data in Brief

    doi: 10.1016/j.dib.2018.01.058

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

    Techniques Used:

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

    Techniques Used:

    11) Product Images from "Molecular strain typing of the yaws pathogen, Treponema pallidum subspecies pertenue"

    Article Title: Molecular strain typing of the yaws pathogen, Treponema pallidum subspecies pertenue

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0203632

    RFLP patterns of T . pallidum subsp. pertenue . (A) The tpr E , G , and J genes were amplified in a nested PCR to produce a mixed amplicon approximately 1830–1848 bp in length. Following PCR, amplicons were digested with the enzyme Mse I and analyzed on an Agilent Bioanalyzer. Two RFLP patterns ( q and r ) were observed among the clinical specimens and laboratory strains analyzed, including those for strains only partially typed (data not shown). The sizes of each fragment were confirmed through sequencing and are indicated in red. The Nichols TPA strain was used as a control for RFLP. The violet and green bands visible in each lane depict the Bioanalyzer kit’s internal control upper and lower bands, respectively. (B) Each of the tpr E , G , and J genes was amplified directly from the genome and sequenced. Regions of the products between the IP6 and IP7 primer annealing sequences were analyzed for Mse I restriction sites for both patterns. Approximate positions of each site (indicated as “M”) are shown. Sizes between each restriction site are listed in red.
    Figure Legend Snippet: RFLP patterns of T . pallidum subsp. pertenue . (A) The tpr E , G , and J genes were amplified in a nested PCR to produce a mixed amplicon approximately 1830–1848 bp in length. Following PCR, amplicons were digested with the enzyme Mse I and analyzed on an Agilent Bioanalyzer. Two RFLP patterns ( q and r ) were observed among the clinical specimens and laboratory strains analyzed, including those for strains only partially typed (data not shown). The sizes of each fragment were confirmed through sequencing and are indicated in red. The Nichols TPA strain was used as a control for RFLP. The violet and green bands visible in each lane depict the Bioanalyzer kit’s internal control upper and lower bands, respectively. (B) Each of the tpr E , G , and J genes was amplified directly from the genome and sequenced. Regions of the products between the IP6 and IP7 primer annealing sequences were analyzed for Mse I restriction sites for both patterns. Approximate positions of each site (indicated as “M”) are shown. Sizes between each restriction site are listed in red.

    Techniques Used: Amplification, Nested PCR, Polymerase Chain Reaction, Sequencing

    Analysis of the arp 60-bp repeat region. (A) A portion of the arp gene was amplified through PCR and run on an Agilent Bioanalyzer for each sample. Seven patterns containing 2, 3, 4, 5, 6, 9, and 10 repeats were identified among the samples tested in the lab, and an additional pattern (12 repeats) was seen following in silico analysis of one of the published genomes (not shown). The Nichols TPA strain, which contains 14 repeats, was used as a reference. The violet and green bands visible in each lane depict the Bioanalyzer kit’s internal control upper and lower bands, respectively. (B) Distribution of repeat sizes in clinical specimens from Vanuatu, Ghana clinical specimens, and among laboratory strains.
    Figure Legend Snippet: Analysis of the arp 60-bp repeat region. (A) A portion of the arp gene was amplified through PCR and run on an Agilent Bioanalyzer for each sample. Seven patterns containing 2, 3, 4, 5, 6, 9, and 10 repeats were identified among the samples tested in the lab, and an additional pattern (12 repeats) was seen following in silico analysis of one of the published genomes (not shown). The Nichols TPA strain, which contains 14 repeats, was used as a reference. The violet and green bands visible in each lane depict the Bioanalyzer kit’s internal control upper and lower bands, respectively. (B) Distribution of repeat sizes in clinical specimens from Vanuatu, Ghana clinical specimens, and among laboratory strains.

    Techniques Used: Amplification, Polymerase Chain Reaction, In Silico

    12) Product Images from "A multidimensional platform for the purification of non-coding RNA species"

    Article Title: A multidimensional platform for the purification of non-coding RNA species

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkt668

    Separation of CCRF-SB and E. coli total RNA by SE-HPLC. ( A ) Typical profile of E. coli total RNA consisting of 23S, 16S rRNAs and co-eluting 5S rRNA and tRNA obtained on a Bio SEC-5 1000 Å column. ( B ) Typical profile of CCRF-SB total RNA consisting of 28S, 18S rRNAs and co-eluting 5.8S, 5S rRNA and tRNA obtained on a Bio SEC-5 1000 Å column. ( C ) Typical profile of E. coli total RNA consisting of 5S rRNA, tRNAs and co-eluting 16S and 23S rRNAs obtained on a Bio SEC-3 300 Å column. ( D ) Typical profile of CCRF-SB total RNA consisting of 5.8S, 5S rRNA, tRNAs and co-eluting 18S and 28S rRNAs obtained on a Bio SEC-3 300 Å column. The chromatograms show the analysis of 10 µg of total RNA extracted using Trizol reagent (Materials and Methods). ( E ) Separation of miRNA, tRNAs, 5.8S, 5S rRNAs, putative snRNAs and snoRNAs, and co-eluting 18S and 28S rRNAs from human lymphoblastic cell line CCRF-SB total RNA by IP RP HPLC obtained on a SOURCE 5RPC ST 4.5/150 column. The identity and purity of the RNAs collected in each fraction was validated with Bioanalyzer RNA 6000 Pico and Small RNA LabChips ( Supplementary Figures S1 and S3 ).
    Figure Legend Snippet: Separation of CCRF-SB and E. coli total RNA by SE-HPLC. ( A ) Typical profile of E. coli total RNA consisting of 23S, 16S rRNAs and co-eluting 5S rRNA and tRNA obtained on a Bio SEC-5 1000 Å column. ( B ) Typical profile of CCRF-SB total RNA consisting of 28S, 18S rRNAs and co-eluting 5.8S, 5S rRNA and tRNA obtained on a Bio SEC-5 1000 Å column. ( C ) Typical profile of E. coli total RNA consisting of 5S rRNA, tRNAs and co-eluting 16S and 23S rRNAs obtained on a Bio SEC-3 300 Å column. ( D ) Typical profile of CCRF-SB total RNA consisting of 5.8S, 5S rRNA, tRNAs and co-eluting 18S and 28S rRNAs obtained on a Bio SEC-3 300 Å column. The chromatograms show the analysis of 10 µg of total RNA extracted using Trizol reagent (Materials and Methods). ( E ) Separation of miRNA, tRNAs, 5.8S, 5S rRNAs, putative snRNAs and snoRNAs, and co-eluting 18S and 28S rRNAs from human lymphoblastic cell line CCRF-SB total RNA by IP RP HPLC obtained on a SOURCE 5RPC ST 4.5/150 column. The identity and purity of the RNAs collected in each fraction was validated with Bioanalyzer RNA 6000 Pico and Small RNA LabChips ( Supplementary Figures S1 and S3 ).

    Techniques Used: High Performance Liquid Chromatography, Size-exclusion Chromatography

    Isolation of ncRNA from P. berghei -infected rodent reticulocytes. ( A ) Bioanalyzer analysis of total RNA extracted from whole blood from uninfected rats (black line) and total RNA extracted from P. berghei schizonts purified from infected rat erythrocytes following lysis of the red blood cells and washing of the schizonts, as described in Supplementary Methods (gray lane). ( B ) 2D-SEC purification of P. berghei ncRNA. Total RNA from schizonts purified from lysed rodent reticulocytes was resolved on the 2D HPLC system, with Bio SEC-3 300 Å resolution of 5.8S rRNA ( 1 ), 5s rRNA ( 2 ), putative snRNA/snoRNA ( 3 ) and tRNA ( 4 ), and Bio SEC-5 1000 Å resolution of the 28s 800 nt rRNA fragment ( 6 ) from the co-eluting 18s rRNA and 28s 3000 nt rRNA fragment ( 5 ). Individual RNA species were collected from the 2-D HPLC elution, and the purity and identity of each fraction was evaluated by Bioanalyzer analysis as shown in Supplementary Figure S6 .
    Figure Legend Snippet: Isolation of ncRNA from P. berghei -infected rodent reticulocytes. ( A ) Bioanalyzer analysis of total RNA extracted from whole blood from uninfected rats (black line) and total RNA extracted from P. berghei schizonts purified from infected rat erythrocytes following lysis of the red blood cells and washing of the schizonts, as described in Supplementary Methods (gray lane). ( B ) 2D-SEC purification of P. berghei ncRNA. Total RNA from schizonts purified from lysed rodent reticulocytes was resolved on the 2D HPLC system, with Bio SEC-3 300 Å resolution of 5.8S rRNA ( 1 ), 5s rRNA ( 2 ), putative snRNA/snoRNA ( 3 ) and tRNA ( 4 ), and Bio SEC-5 1000 Å resolution of the 28s 800 nt rRNA fragment ( 6 ) from the co-eluting 18s rRNA and 28s 3000 nt rRNA fragment ( 5 ). Individual RNA species were collected from the 2-D HPLC elution, and the purity and identity of each fraction was evaluated by Bioanalyzer analysis as shown in Supplementary Figure S6 .

    Techniques Used: Isolation, Infection, Purification, Lysis, Size-exclusion Chromatography, High Performance Liquid Chromatography

    The 2D-SEC of BCG total RNA preserves the native post-transcriptional ribonucleoside modifications in purified tRNA. ( A ) Baseline separation of BCG total RNA to its component 23S (insert 1), 16S (insert 2), 5S rRNAs (insert 3) and tRNA (insert 4) obtained on a Bio SEC-5 1000 Å (column 1) and Bio SEC-3 300 Å (column 2) two-column online HPLC system (ID 7.8 mm, 300 mm for each column) demonstrating the purity and quality of each RNA species based on sequence lengths on the Bioanalyzer RNA 6000 Pico and Small RNA LabChips. ( B ) Extracted ion chromatograms of naturally occurring modified ribonucleosides in hydrolyzed BCG tRNA identified by HPLC-coupled triple quadrupole mass spectrometry in multiple reaction monitoring mode. The peaks of m 1 A (2.87 min) and m 7 G (4.53 min) are marked with ‘//’ to indicate that they are in different scales from other peaks. Identities of the 18 post-transcriptional modifications detected are shown in Supplementary Table S2 . Inset: MS/MS validation of N 6 ,N 6 -dimethyladenosine ( ). Ribonucleoside with m/z of 296.1356 was targeted for CID fragmentation on a high mass accuracy quadrupole time-of-flight mass spectrometer yielding a daughter ion with m/z 164.0927.
    Figure Legend Snippet: The 2D-SEC of BCG total RNA preserves the native post-transcriptional ribonucleoside modifications in purified tRNA. ( A ) Baseline separation of BCG total RNA to its component 23S (insert 1), 16S (insert 2), 5S rRNAs (insert 3) and tRNA (insert 4) obtained on a Bio SEC-5 1000 Å (column 1) and Bio SEC-3 300 Å (column 2) two-column online HPLC system (ID 7.8 mm, 300 mm for each column) demonstrating the purity and quality of each RNA species based on sequence lengths on the Bioanalyzer RNA 6000 Pico and Small RNA LabChips. ( B ) Extracted ion chromatograms of naturally occurring modified ribonucleosides in hydrolyzed BCG tRNA identified by HPLC-coupled triple quadrupole mass spectrometry in multiple reaction monitoring mode. The peaks of m 1 A (2.87 min) and m 7 G (4.53 min) are marked with ‘//’ to indicate that they are in different scales from other peaks. Identities of the 18 post-transcriptional modifications detected are shown in Supplementary Table S2 . Inset: MS/MS validation of N 6 ,N 6 -dimethyladenosine ( ). Ribonucleoside with m/z of 296.1356 was targeted for CID fragmentation on a high mass accuracy quadrupole time-of-flight mass spectrometer yielding a daughter ion with m/z 164.0927.

    Techniques Used: Size-exclusion Chromatography, Purification, High Performance Liquid Chromatography, Sequencing, Modification, Mass Spectrometry

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

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

    Journal: Journal of Extracellular Vesicles

    doi: 10.3402/jev.v5.30281

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

    Techniques Used: Chromatin Immunoprecipitation, Marker, Fluorescence

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

    Techniques Used: Isolation, Marker

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

    Techniques Used: Chromatin Immunoprecipitation, Marker, Fluorescence

    14) Product Images from "Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling"

    Article Title: Expression microarray reproducibility is improved by optimising purification steps in RNA amplification and labelling

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-5-9

    Effect of aRNA purity and labelled-aRNA purification . (A) Graph showing coupling efficiency (C) and 320/650 (B) values for six MCF-7 aRNA samples with different 260/280 ratios. (B) Agilent Bioanalyzer pattern of MCF-7 Cy5-labelled target using an aRNA with 260/280 ratio of 1.6. Sharp spikes represent uncoupled Cy5 dye. (C) Same as B for aRNA with 260/280 ratio of 2 and coupling efficiency near 1. (D) NanoDrop ® ND-1000 Spectrophotometer absorptions at 320 and 650 nm wavelengths of a MCF-7 Cy5-labelled target. 320/650 ratio-0.6. (E) Same as in d (different sample). 320/650 ratio-0.09. (F) Recovery rates (R) and coupling efficiencies (C) for different labelled-aRNA purification methods. Data is presented for MCF-7 cell line and measurements represent an average of three separate reactions. Li-ETOH – LiCl-ethanol; PCI – phenol/chloroform/isoamyl alcohol.
    Figure Legend Snippet: Effect of aRNA purity and labelled-aRNA purification . (A) Graph showing coupling efficiency (C) and 320/650 (B) values for six MCF-7 aRNA samples with different 260/280 ratios. (B) Agilent Bioanalyzer pattern of MCF-7 Cy5-labelled target using an aRNA with 260/280 ratio of 1.6. Sharp spikes represent uncoupled Cy5 dye. (C) Same as B for aRNA with 260/280 ratio of 2 and coupling efficiency near 1. (D) NanoDrop ® ND-1000 Spectrophotometer absorptions at 320 and 650 nm wavelengths of a MCF-7 Cy5-labelled target. 320/650 ratio-0.6. (E) Same as in d (different sample). 320/650 ratio-0.09. (F) Recovery rates (R) and coupling efficiencies (C) for different labelled-aRNA purification methods. Data is presented for MCF-7 cell line and measurements represent an average of three separate reactions. Li-ETOH – LiCl-ethanol; PCI – phenol/chloroform/isoamyl alcohol.

    Techniques Used: Purification, Spectrophotometry

    Effect of genomic DNA contamination in total RNA . (A) 1% agarose gel of purified MCF-7 total RNA samples. L-1 kb ladder (Invitrogen); Col. – column purified RNA; D20 – DNase treated/PCI extracted (RNA concentration – 20 μg/100 μl); D5 – DNase treated/PCI extracted (RNA concentration – 5 μg/100 μl); LiCl – DNase treated/Lithium Chloride purified. (B) Agilent Bioanalyzer image of MCF-7 total RNA sample purified using column method. Arrow pointing at shoulder after 28S band indicating genomic DNA carry over. (C) 1% agarose/formamide denaturing gel of MCF-7 aRNA. L1 – 6000 RNA ladder (Ambion); L2-1 Kb ladder (Invitrogen). (D) Absorption at 260 nm of nucleic acid products derived from the 4 total RNA purification methods. 2 μg of total RNA from each of the five cell lines was amplified with and without reverse transcriptase being added to the cDNA synthesis reaction (with RT and no RT respectively). C – column; Li – LiCl precipitation; D5/D20 – as in A. Cell lines included MCF-7, ZR-75-1-1, OCUB-M, Cal51, and HCT-1187.
    Figure Legend Snippet: Effect of genomic DNA contamination in total RNA . (A) 1% agarose gel of purified MCF-7 total RNA samples. L-1 kb ladder (Invitrogen); Col. – column purified RNA; D20 – DNase treated/PCI extracted (RNA concentration – 20 μg/100 μl); D5 – DNase treated/PCI extracted (RNA concentration – 5 μg/100 μl); LiCl – DNase treated/Lithium Chloride purified. (B) Agilent Bioanalyzer image of MCF-7 total RNA sample purified using column method. Arrow pointing at shoulder after 28S band indicating genomic DNA carry over. (C) 1% agarose/formamide denaturing gel of MCF-7 aRNA. L1 – 6000 RNA ladder (Ambion); L2-1 Kb ladder (Invitrogen). (D) Absorption at 260 nm of nucleic acid products derived from the 4 total RNA purification methods. 2 μg of total RNA from each of the five cell lines was amplified with and without reverse transcriptase being added to the cDNA synthesis reaction (with RT and no RT respectively). C – column; Li – LiCl precipitation; D5/D20 – as in A. Cell lines included MCF-7, ZR-75-1-1, OCUB-M, Cal51, and HCT-1187.

    Techniques Used: Agarose Gel Electrophoresis, Purification, Concentration Assay, Derivative Assay, Amplification

    Analysis of aRNA purification . (A) Amplified RNA yields and 260/280 ratios with 4 methods of purification. Col – column; PCI – phenol/chlorform/isoamyl alchohol; LiCl – 2.5 M LiCl; G-P – guanidinium-phenol. (B) 1% denaturing agarose/formamide gel of MCF-7 aRNA purified using column (C) Agilent Bioanalyzer analysis of aRNA (from MCF-7) purified by G-P. 6000 nano marker from Ambion (blue) superimposed on the RNA trace. (D) Plot of aRNA yield in μg for different starting total RNA quantities. C1 – OCUB-M with Col.; L1 – OCUB-M with LiCl; G1 – OCUB-M with G-P; C2 – MCF-7 with Col.; L2 – MCF-7 with LiCl; G2 – MCF-7 with G-P.
    Figure Legend Snippet: Analysis of aRNA purification . (A) Amplified RNA yields and 260/280 ratios with 4 methods of purification. Col – column; PCI – phenol/chlorform/isoamyl alchohol; LiCl – 2.5 M LiCl; G-P – guanidinium-phenol. (B) 1% denaturing agarose/formamide gel of MCF-7 aRNA purified using column (C) Agilent Bioanalyzer analysis of aRNA (from MCF-7) purified by G-P. 6000 nano marker from Ambion (blue) superimposed on the RNA trace. (D) Plot of aRNA yield in μg for different starting total RNA quantities. C1 – OCUB-M with Col.; L1 – OCUB-M with LiCl; G1 – OCUB-M with G-P; C2 – MCF-7 with Col.; L2 – MCF-7 with LiCl; G2 – MCF-7 with G-P.

    Techniques Used: Purification, Amplification, Marker

    15) Product Images from "Assessment of Circulating LncRNAs Under Physiologic and Pathologic Conditions in Humans Reveals Potential Limitations as Biomarkers"

    Article Title: Assessment of Circulating LncRNAs Under Physiologic and Pathologic Conditions in Humans Reveals Potential Limitations as Biomarkers

    Journal: Scientific Reports

    doi: 10.1038/srep36596

    Characterization and confirmation of RNA quality. ( a ) Concentration of total RNA extracted from plasma as measured by Nanodrop spectrophotometry. Two mock RNA extractions performed with ddH2O instead of plasma, highlight the lower limit of detection. ( b ) Relative levels of other endogenous plasma RNA species that were extracted and measured in parallel using the same pre-amplification and RT-PCR platform as the lncRNAs. ( c ) Relative levels of several representative miRNAs that were detected without pre-amplification from the same extracted total RNA. ( d ) A fixed quantity of synthetic 22 nt miRNA mimic (cel-miR-39) with no homology to mammalian miRNAs was spiked into plasma samples just after chemical denaturation of the endogenous RNases. Relative levels are shown for duplicate measurements in eight control subjects. ( e ) No significant correlation observed between the age of plasma specimens and the number of detected lncRNAs. Pearson correlation coefficient and p-value are shown. ( f ) No significant correlation observed between plasma specimen age and two specific lncRNAs that were detectable in all subjects. ( g ) Agilent bioanalzyer electropherogram showing fragment patterns of RNA derived from three different lung tissue specimens (L1-L3) before and after mock RNA extractions. 18s and 28s ribosomal bands are indicated. ( h ) Agilent bioanalyzer RNA integrity numbers are shown for each RNA sample (L1-L3) before and after the mock extractions. Integrity levels vary from 0 (highly degraded) to 10 (highly intact). Circles denote control subjects and squares denote PAH patients.
    Figure Legend Snippet: Characterization and confirmation of RNA quality. ( a ) Concentration of total RNA extracted from plasma as measured by Nanodrop spectrophotometry. Two mock RNA extractions performed with ddH2O instead of plasma, highlight the lower limit of detection. ( b ) Relative levels of other endogenous plasma RNA species that were extracted and measured in parallel using the same pre-amplification and RT-PCR platform as the lncRNAs. ( c ) Relative levels of several representative miRNAs that were detected without pre-amplification from the same extracted total RNA. ( d ) A fixed quantity of synthetic 22 nt miRNA mimic (cel-miR-39) with no homology to mammalian miRNAs was spiked into plasma samples just after chemical denaturation of the endogenous RNases. Relative levels are shown for duplicate measurements in eight control subjects. ( e ) No significant correlation observed between the age of plasma specimens and the number of detected lncRNAs. Pearson correlation coefficient and p-value are shown. ( f ) No significant correlation observed between plasma specimen age and two specific lncRNAs that were detectable in all subjects. ( g ) Agilent bioanalzyer electropherogram showing fragment patterns of RNA derived from three different lung tissue specimens (L1-L3) before and after mock RNA extractions. 18s and 28s ribosomal bands are indicated. ( h ) Agilent bioanalyzer RNA integrity numbers are shown for each RNA sample (L1-L3) before and after the mock extractions. Integrity levels vary from 0 (highly degraded) to 10 (highly intact). Circles denote control subjects and squares denote PAH patients.

    Techniques Used: Concentration Assay, Spectrophotometry, Amplification, Reverse Transcription Polymerase Chain Reaction, Derivative Assay

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

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

    Journal: Frontiers in Genetics

    doi: 10.3389/fgene.2018.00006

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

    Techniques Used:

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

    Techniques Used: Isolation, Purification, Molecular Weight

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

    Techniques Used: Concentration Assay, Mouse Assay, Molecular Weight

    17) Product Images from "PCR amplification of a triple-repeat genetic target directly from whole blood in 15 minutes as a proof-of-principle PCR study for direct sample analysis for a clinically relevant target"

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

    Journal: BMC Medical Genetics

    doi: 10.1186/s12881-014-0130-5

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

    Techniques Used: Purification

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

    Techniques Used: Polymerase Chain Reaction, Purification, Marker

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

    Techniques Used: Purification, Marker

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

    Techniques Used: Purification

    18) Product Images from "Comparison of target labeling methods for use with Affymetrix GeneChips"

    Article Title: Comparison of target labeling methods for use with Affymetrix GeneChips

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-7-24

    Overlaid Bioanalyzer electropherograms for fragmented labeled cRNA targets showing the size distribution of fragmented target. One-Cycle replicates (blue and green); Superscript replicates (orange and black); BioArray replicates (pink and turquoise). RNA ladder in red showing the lower alignment marker and the 200 and 500 base markers.
    Figure Legend Snippet: Overlaid Bioanalyzer electropherograms for fragmented labeled cRNA targets showing the size distribution of fragmented target. One-Cycle replicates (blue and green); Superscript replicates (orange and black); BioArray replicates (pink and turquoise). RNA ladder in red showing the lower alignment marker and the 200 and 500 base markers.

    Techniques Used: Labeling, Marker

    Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).
    Figure Legend Snippet: Overlaid electropherograms from the analysis of unfragmented biotinylated cRNA products from the IVT reactions of the 3 different labeling kits by the Agilent 2100 Bioanalyzer. The replicate reactions from donor A are shown for each kit: One-Cycle data represented as blue and green line; BioArray as black and orange and Superscript by the pink and turquoise lines. 1 μl of the final volume (One-Cycle = 21 μl; BioArray = 60 μl; Superscript = 100 μl) of purified IVT reaction is loaded. The RNA ladder (peaks represented in red) contains a mixture of RNAs of known concentration and size (50 (lower marker) 200, 500, 1,000, 2,000, 4,000, and 6,000 bases from left to right).

    Techniques Used: Labeling, Purification, Concentration Assay, Marker

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

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

    Journal: Journal of Extracellular Vesicles

    doi: 10.3402/jev.v5.30281

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

    Techniques Used: Chromatin Immunoprecipitation, Marker, Fluorescence

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

    Techniques Used: Isolation, Marker

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

    Techniques Used: Chromatin Immunoprecipitation, Marker, Fluorescence

    20) Product Images from "Fluorescent labeling of CRISPR/Cas9 RNP for gene knockout in HSPCs and iPSCs reveals an essential role for GADD45b in stress response"

    Article Title: Fluorescent labeling of CRISPR/Cas9 RNP for gene knockout in HSPCs and iPSCs reveals an essential role for GADD45b in stress response

    Journal: Blood Advances

    doi: 10.1182/bloodadvances.2017015511

    Scheme of CRISPR/Cas9–gRNA RNP labeling and cell transfection. (A) crRNA and tracrRNA were annealed at room temperature for 10 minutes. The resulting gRNA was labeled with fluorescein- or CX-rhodamine–coupled Label IT Tracker labeling reagent. The fluorescent GADD45B -targeting gRNA was assembled with recombinant Cas9 protein prior to transfection to assemble an active CRISPR/Cas9–gRNA RNP complex targeting human GADD45B . Cells were transfected with TransIT-X2 Transfection Reagent or by using the Amaxa Nucleofector System and were incubated for 24 hours before sorting the CX-rhodamine+ or fluorescein+ cells using a BD FACSAria II. After sorting, some of the cells were used for a single-cell culture, and the rest were used for DNA isolation or cell-based assays. (B) Virtual gel of an Agilent Bioanalyzer analysis revealing no difference in the size or quality of labeled gRNA compared with unlabeled gRNA. (C) GADD45B was targeted using gRNA (highlighted in red), which inserts a double-strand break at NM_015675.3 exon 1, 31 bp after ATG; NP_056490.2, p.N11.
    Figure Legend Snippet: Scheme of CRISPR/Cas9–gRNA RNP labeling and cell transfection. (A) crRNA and tracrRNA were annealed at room temperature for 10 minutes. The resulting gRNA was labeled with fluorescein- or CX-rhodamine–coupled Label IT Tracker labeling reagent. The fluorescent GADD45B -targeting gRNA was assembled with recombinant Cas9 protein prior to transfection to assemble an active CRISPR/Cas9–gRNA RNP complex targeting human GADD45B . Cells were transfected with TransIT-X2 Transfection Reagent or by using the Amaxa Nucleofector System and were incubated for 24 hours before sorting the CX-rhodamine+ or fluorescein+ cells using a BD FACSAria II. After sorting, some of the cells were used for a single-cell culture, and the rest were used for DNA isolation or cell-based assays. (B) Virtual gel of an Agilent Bioanalyzer analysis revealing no difference in the size or quality of labeled gRNA compared with unlabeled gRNA. (C) GADD45B was targeted using gRNA (highlighted in red), which inserts a double-strand break at NM_015675.3 exon 1, 31 bp after ATG; NP_056490.2, p.N11.

    Techniques Used: CRISPR, Labeling, Transfection, Recombinant, Incubation, Cell Culture, DNA Extraction

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    Western Blot:

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    Gas Chromatography:

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    Polymerase Chain Reaction:

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    Hybridization:

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    Article Snippet: The third QC step verifies that enough DNA is retained from the hybridization and amplification steps in a second PCR and that the size of the resulting final library is in the optimum range for paired-end sequencing. .. Parameters that are quantified from readings of the Bioanalyzer (DNA 1000 assay) (Agilent; Waldbronn, Germany) platform include amount of sheared DNA and the smallest and largest fragment size of the sheared DNA; the amount of DNA after the pre-PCR and the smallest and largest fragment sizes of the resulting DNA; as well as the amount of final library and the smallest and largest fragment size of remaining DNA.

    Multiplexing:

    Article Title: Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester
    Article Snippet: After 16S rDNA gene amplification, the multiplexing step was performed using a Nextera XT Index Kit (Illumina, San Diego, CA, USA). .. One microliter of the PCR product was checked with a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA) and libraries were prepared using a 2x300pb paired-end run (MiSeq Reagent kit v3) according to manufacturer’s instructions (Illumina) at FISABIO sequencing service (Valencia, Spain).

    Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
    Article Snippet: For the addition of multiplexing index-sequences to the overhang adapters, a second-step PCR was performed using a 384 libraries Nextera XT index kit v2 (Illumina). .. Thermal cycling conditions were 96°C for 3 min, followed by 8 cycles of 95°C for 30 s, 55°C for 30 s and 72°C for 30 s, with a final extension of 72°C for 5 min. Amplicon sizes (464 bp) of randomly selected sampled were then analyzed by Bioanalyzer DNA 1000 chip (Agilent Technologies).

    Article Title: HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa
    Article Snippet: The V3-V4 region of 16S rDNA gene was amplified by PCR using Illumina adapter overhang nucleotide sequences following Illumina protocols. .. After 16S rDNA gene amplification, the multiplexing step was performed using Nextera XT Index Kit (Illumina, San Diego, CA, USA) and PCR product was checked in a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA). .. Libraries were sequenced using a 2 × 300 pb paired-end run (MiSeq Reagent kit v3) on a MiSeq-Illumina platform (Lifesequencing sequencing service, Valencia, Spain).

    Sensitive Assay:

    Article Title: Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F)
    Article Snippet: The optimum annealing temperature for the Illumina-adapted primers was determined by performing temperature gradient PCRs (53–65°C, 0.5°C steps) and the annealing step in the amplicon PCR was set at 58°C thereafter. .. Following the second, indexing PCR and final product purification, amplicon libraries were quantified with the Qubit dsDNA High Sensitivity Assay (Qubit 3.0, ThermoFisher) and the amplicon size was determined with the Bioanalyzer High Sensitivity DNA Assay (Agilent). .. Amplicon libraries were then submitted to the Okinawa Institute of Science and Technology (OIST) sequencing center for 300 × 300-bp paired-end sequencing on the Illumina MiSeq sequencing platform with v3 chemistry.

    Methylation:

    Article Title: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
    Article Snippet: Paragraph title: Methylation sequencing ... Fragment size was controlled on a Bioanalyzer DNA 1000 Chip (Agilent) and the KAPA High Throughput Library Preparation Kit (KAPA Biosystems) was applied.

    Isolation:

    Article Title: Single-Cell Semiconductor Sequencing
    Article Snippet: Size of the band isolation is dependent on the templating and sequencing kits. .. Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ).

    Article Title: Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester
    Article Snippet: Total DNA was isolated from fecal samples using a commercially available kit, InviMag® Stool DNA kit (Invitek GmbH, Berlin, Germany), in the KingFisher magnetic particle processor (Thermo Electron, Vantaa, Finland) as described previously [ ]. .. One microliter of the PCR product was checked with a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA) and libraries were prepared using a 2x300pb paired-end run (MiSeq Reagent kit v3) according to manufacturer’s instructions (Illumina) at FISABIO sequencing service (Valencia, Spain).

    Article Title: HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa
    Article Snippet: Isolated DNA concentrations were measured using a Qubit® 2.0 Fluorometer (Life Technology, Carlsbad, CA, USA) and normalized to10 ng/μL. .. After 16S rDNA gene amplification, the multiplexing step was performed using Nextera XT Index Kit (Illumina, San Diego, CA, USA) and PCR product was checked in a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA).

    Purification:

    Article Title: Single-Cell Semiconductor Sequencing
    Article Snippet: The amplified PCR product is purified with 1.8 volumes of AMPure XP Reagent (450 μL) as described above and eluted with 20 μL of Nuclease-free water. .. Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ).

    Article Title: Altered gut metabolome contributes to depression-like behaviors in rats exposed to chronic unpredictable mild stress
    Article Snippet: The PCR cycling conditions were as follows: 98 °C for 30 s, followed by 35 cycles of 98 °C for 5 s, 56 °C for 20 s, and 70 °C for 20 s. The PCR amplicons were purified with AmpureXp beads (AGENCOURT) to remove nonspecific products. .. PCR products were checked using a Bioanalyzer DNA 1000 chip (Agilent Technologies, CA, USA), and libraries were qualified and pair-end sequenced using the PE300 sequencing strategy provided by the Illumina MiSeq system.

    Article Title: Association of prevalent vaginal microbiome of mother with occurrence of type I diabetes in child
    Article Snippet: Triplicate PCR reactions were performed, each containing 1x Phusion GC buffer, 0.4 µM of the forward and reverse primers, 200 µM dNTPs, 0.5 U of Phusion enzyme (Finnzymes, Finland) and 10 ng of genomic community DNA as the template, together with molecular-grade water in a total reaction volume of 20 µl. .. The triplicate pooled PCR amplified reactions were purified using the AMPure XP PCR clean-up kit (Agencourt Bioscience, CA, USA) and the DNA concentration was measured on a Bioanalyzer DNA chip (Agilent Technologies, CA, USA). .. Individual samples were pooled in an equivalent amount, size selected using BluePippin automated electrophoresis system (Sage Science, MA, USA) on 1.5% agarose gel, twice purified with AMPure XP kit, final DNA concentration was measured using Bioanalyzer DNA chip and sequenced on a 316 v2 chip using Ion Torrent 400 bp chemistry (Life Technologies, USA) using to 15 pM sample concentration.

    Article Title: Characterization of circulating transfer RNA-derived RNA fragments in cattle
    Article Snippet: After the gel was run the pools were concentrated using the QIAquick PCR purification kit (QIAGEN, Germantown, MD, USA) by eluting in 32 ul of RNase free water. .. One microliter of the size selected library pool was run using a High sensitivity DNA chip Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester
    Article Snippet: Purified DNA was determined using a Qubit® 2.0 Fluorometer (Life Technology, Carlsbad, CA, USA) and normalized to 5 ng/μL for amplicon libraries. .. One microliter of the PCR product was checked with a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA) and libraries were prepared using a 2x300pb paired-end run (MiSeq Reagent kit v3) according to manufacturer’s instructions (Illumina) at FISABIO sequencing service (Valencia, Spain).

    Article Title: Gut Microbiota Features in Young Children With Autism Spectrum Disorders
    Article Snippet: After each PCR step, amplicons were purified with Agencourt AMPure XP beads (Beckman Coulter Inc.). .. Then, library sizes and concentrations of barcoded amplicons were assessed using Bioanalyzer DNA 1000 chip (Agilent technologies) and Qubit dsDNA BR assay kit (Invitrogen), respectively.

    Article Title: The microbiome in PTEN hamartoma tumor syndrome
    Article Snippet: Indexed PCR products were purified with Ampure XP beads (Beckman Coulter, Brea, CA, USA) and quantified with Qubit dsDNA system (ThermoFisher Scientific). .. Samples were then normalized and pooled into sequencing libraries at 20 nM for oral wash and fecal samples and 1 nM for urine samples, then validated on a Bioanalyzer DNA 1000 chip (Agilent) and sequenced on the Illumina MiSeq with a V3 reagent kit at the Case Western Reserve University Genomics Core Facility.

    Article Title: Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F)
    Article Snippet: The optimum annealing temperature for the Illumina-adapted primers was determined by performing temperature gradient PCRs (53–65°C, 0.5°C steps) and the annealing step in the amplicon PCR was set at 58°C thereafter. .. Following the second, indexing PCR and final product purification, amplicon libraries were quantified with the Qubit dsDNA High Sensitivity Assay (Qubit 3.0, ThermoFisher) and the amplicon size was determined with the Bioanalyzer High Sensitivity DNA Assay (Agilent). .. Amplicon libraries were then submitted to the Okinawa Institute of Science and Technology (OIST) sequencing center for 300 × 300-bp paired-end sequencing on the Illumina MiSeq sequencing platform with v3 chemistry.

    Article Title: Loss of eIF4E Phosphorylation Engenders Depression-like Behaviors via Selective mRNA Translation
    Article Snippet: Purified RNA was eluted from the beads and mixed with an equal volume of 2× alkaline fragmentation solution (2 m m EDTA, 10 m m Na2 CO3 , 90 m m NaHCO3 , pH 9.2) and incubated for 20 min at 95°C. .. All samples were analyzed on a Bioanalyzer High Sensitivity DNA chip (Agilent Technologies) to confirm expected size range and quantity and sequenced on a HiSeq 2500 system (Illumina).

    Article Title: Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity
    Article Snippet: The products were purified using the QIAquick PCR Purification Kit (Qiagen) to construct an Illumina paired end library. .. Library quality control was performed with a Bioanalyzer DNA 1000 Chip Series II (Agilent).

    Sequencing:

    Article Title: AR intragenic deletions linked to androgen receptor splice variant expression and activity in models of prostate cancer progression
    Article Snippet: Paragraph title: Paired-end library creation, sequence capture, and next-generation sequencing ... A Bioanalyzer DNA 1000 chip (Agilent, Santa Clara, CA) was used to verify DNA samples sheared with fragment peaks between 150-200 bp.

    Article Title: Single-Cell Semiconductor Sequencing
    Article Snippet: For 200 bp templating and sequencing kits, the sequencing library cannot be > 320 bp. .. Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ).

    Article Title: Altered gut metabolome contributes to depression-like behaviors in rats exposed to chronic unpredictable mild stress
    Article Snippet: The PCR cycling conditions were as follows: 98 °C for 30 s, followed by 35 cycles of 98 °C for 5 s, 56 °C for 20 s, and 70 °C for 20 s. The PCR amplicons were purified with AmpureXp beads (AGENCOURT) to remove nonspecific products. .. PCR products were checked using a Bioanalyzer DNA 1000 chip (Agilent Technologies, CA, USA), and libraries were qualified and pair-end sequenced using the PE300 sequencing strategy provided by the Illumina MiSeq system. .. For GC–MS, mass data were collected in full scan mode from 50 to 650 m/z.

    Article Title: Association of prevalent vaginal microbiome of mother with occurrence of type I diabetes in child
    Article Snippet: The F519 primer contained an Ion Torrent pyrosequencing adapter sequence A (Lifescience Technologies, USA), a 9-bp unique barcode sequence and one nucleotide linker, while the R926 primer contained an Ion Torrent adapter trP1 sequence. .. The triplicate pooled PCR amplified reactions were purified using the AMPure XP PCR clean-up kit (Agencourt Bioscience, CA, USA) and the DNA concentration was measured on a Bioanalyzer DNA chip (Agilent Technologies, CA, USA).

    Article Title: Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester
    Article Snippet: After 16S rDNA gene amplification, the multiplexing step was performed using a Nextera XT Index Kit (Illumina, San Diego, CA, USA). .. One microliter of the PCR product was checked with a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA) and libraries were prepared using a 2x300pb paired-end run (MiSeq Reagent kit v3) according to manufacturer’s instructions (Illumina) at FISABIO sequencing service (Valencia, Spain). .. All clinical data from individual participants were combined according to their pre-BMI in normoweight (N/W), overweight (O/W), and obese (O/O) groups.

    Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
    Article Snippet: Paragraph title: Amplicon sequencing samples preparation and data analysis ... Thermal cycling conditions were 96°C for 3 min, followed by 8 cycles of 95°C for 30 s, 55°C for 30 s and 72°C for 30 s, with a final extension of 72°C for 5 min. Amplicon sizes (464 bp) of randomly selected sampled were then analyzed by Bioanalyzer DNA 1000 chip (Agilent Technologies).

    Article Title: Gut Microbiota Features in Young Children With Autism Spectrum Disorders
    Article Snippet: Paragraph title: V3–V4 16S rRNA Gene Sequencing and Data Analysis ... Then, library sizes and concentrations of barcoded amplicons were assessed using Bioanalyzer DNA 1000 chip (Agilent technologies) and Qubit dsDNA BR assay kit (Invitrogen), respectively.

    Article Title: The microbiome in PTEN hamartoma tumor syndrome
    Article Snippet: Indexed PCR products were purified with Ampure XP beads (Beckman Coulter, Brea, CA, USA) and quantified with Qubit dsDNA system (ThermoFisher Scientific). .. Samples were then normalized and pooled into sequencing libraries at 20 nM for oral wash and fecal samples and 1 nM for urine samples, then validated on a Bioanalyzer DNA 1000 chip (Agilent) and sequenced on the Illumina MiSeq with a V3 reagent kit at the Case Western Reserve University Genomics Core Facility. .. Paired-end reads, which were 250 bp in length, were merged with FLASH ( ).

    Article Title: Intra-host Symbiont Diversity and Extended Symbiont Maintenance in Photosymbiotic Acantharea (Clade F)
    Article Snippet: Paragraph title: Library Preparation and Sequencing ... Following the second, indexing PCR and final product purification, amplicon libraries were quantified with the Qubit dsDNA High Sensitivity Assay (Qubit 3.0, ThermoFisher) and the amplicon size was determined with the Bioanalyzer High Sensitivity DNA Assay (Agilent).

    Article Title: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
    Article Snippet: Paragraph title: Methylation sequencing ... Fragment size was controlled on a Bioanalyzer DNA 1000 Chip (Agilent) and the KAPA High Throughput Library Preparation Kit (KAPA Biosystems) was applied.

    Article Title: Neurexins 1–3 Each Have a Distinct Pattern of Expression in the Early Developing Human Cerebral Cortex
    Article Snippet: Full details of the origins, collection, preparation, sequencing, and analysis of the human fetal RNA samples are provided by . .. The size profile of approximately 15% of the libraries was evaluated using an Agilent Bioanalyzer DNA 1000 chip.

    Article Title: The Role of Quality Control in Targeted Next-generation Sequencing Library Preparation
    Article Snippet: The third QC step verifies that enough DNA is retained from the hybridization and amplification steps in a second PCR and that the size of the resulting final library is in the optimum range for paired-end sequencing. .. Parameters that are quantified from readings of the Bioanalyzer (DNA 1000 assay) (Agilent; Waldbronn, Germany) platform include amount of sheared DNA and the smallest and largest fragment size of the sheared DNA; the amount of DNA after the pre-PCR and the smallest and largest fragment sizes of the resulting DNA; as well as the amount of final library and the smallest and largest fragment size of remaining DNA.

    Article Title: HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa
    Article Snippet: Paragraph title: 16S bacterial gene sequencing ... After 16S rDNA gene amplification, the multiplexing step was performed using Nextera XT Index Kit (Illumina, San Diego, CA, USA) and PCR product was checked in a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Isolation and characterization of human osteoblasts from needle biopsies without in vitro culture
    Article Snippet: Following amplification, the products were modified by random priming and extension to create double-stranded products that were suitable for generating libraries for sequencing. .. The concentration and size distribution of the resulting libraries was determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA).

    Article Title: Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity
    Article Snippet: Paragraph title: Library construction and Illumina sequencing ... Library quality control was performed with a Bioanalyzer DNA 1000 Chip Series II (Agilent).

    Agarose Gel Electrophoresis:

    Article Title: Single-Cell Semiconductor Sequencing
    Article Snippet: Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ). .. Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ).

    Article Title: Altered gut metabolome contributes to depression-like behaviors in rats exposed to chronic unpredictable mild stress
    Article Snippet: DNA integrity tests were performed by agarose gel electrophoresis. .. PCR products were checked using a Bioanalyzer DNA 1000 chip (Agilent Technologies, CA, USA), and libraries were qualified and pair-end sequenced using the PE300 sequencing strategy provided by the Illumina MiSeq system.

    Article Title: Characterization of circulating transfer RNA-derived RNA fragments in cattle
    Article Snippet: The pool was then size selected using the Pippin Prep on a 3% Agarose gel without added Ethidium Bromide (SAGE Sciences, Beverly, MA, USA) with a size selection of 142–170 nt according to manufactures instructions. .. One microliter of the size selected library pool was run using a High sensitivity DNA chip Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: The microbiome in PTEN hamartoma tumor syndrome
    Article Snippet: The resulting 16S rDNA amplicons were run on a 1% agarose gel, size-selected at 450–500 bp and gel-purified using QIAquick Gel Purification kit (Qiagen). .. Samples were then normalized and pooled into sequencing libraries at 20 nM for oral wash and fecal samples and 1 nM for urine samples, then validated on a Bioanalyzer DNA 1000 chip (Agilent) and sequenced on the Illumina MiSeq with a V3 reagent kit at the Case Western Reserve University Genomics Core Facility.

    Chromatin Immunoprecipitation:

    Article Title: AR intragenic deletions linked to androgen receptor splice variant expression and activity in models of prostate cancer progression
    Article Snippet: Genomic DNA from CWR22Pc, 22Rv1, and CWR-R1 cells was fragmented using an S220 ultra-sonicator (Covaris, Woburn, MA) with Agilent SureSelect parameters. .. A Bioanalyzer DNA 1000 chip (Agilent, Santa Clara, CA) was used to verify DNA samples sheared with fragment peaks between 150-200 bp. .. Paired-end sequencing libraries were generated from sheared DNA samples using a SureSelect Library Preparation Kit (Agilent) and amplified for sequence capture as per the manufacturer’s protocol.

    Article Title: Single-Cell Semiconductor Sequencing
    Article Snippet: For 200 bp templating and sequencing kits, the sequencing library cannot be > 320 bp. .. Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ). .. If sample concentration is adequate, the sample is ready for emulsion PCR.

    Article Title: Altered gut metabolome contributes to depression-like behaviors in rats exposed to chronic unpredictable mild stress
    Article Snippet: The PCR cycling conditions were as follows: 98 °C for 30 s, followed by 35 cycles of 98 °C for 5 s, 56 °C for 20 s, and 70 °C for 20 s. The PCR amplicons were purified with AmpureXp beads (AGENCOURT) to remove nonspecific products. .. PCR products were checked using a Bioanalyzer DNA 1000 chip (Agilent Technologies, CA, USA), and libraries were qualified and pair-end sequenced using the PE300 sequencing strategy provided by the Illumina MiSeq system. .. For GC–MS, mass data were collected in full scan mode from 50 to 650 m/z.

    Article Title: Association of prevalent vaginal microbiome of mother with occurrence of type I diabetes in child
    Article Snippet: Triplicate PCR reactions were performed, each containing 1x Phusion GC buffer, 0.4 µM of the forward and reverse primers, 200 µM dNTPs, 0.5 U of Phusion enzyme (Finnzymes, Finland) and 10 ng of genomic community DNA as the template, together with molecular-grade water in a total reaction volume of 20 µl. .. The triplicate pooled PCR amplified reactions were purified using the AMPure XP PCR clean-up kit (Agencourt Bioscience, CA, USA) and the DNA concentration was measured on a Bioanalyzer DNA chip (Agilent Technologies, CA, USA). .. Individual samples were pooled in an equivalent amount, size selected using BluePippin automated electrophoresis system (Sage Science, MA, USA) on 1.5% agarose gel, twice purified with AMPure XP kit, final DNA concentration was measured using Bioanalyzer DNA chip and sequenced on a 316 v2 chip using Ion Torrent 400 bp chemistry (Life Technologies, USA) using to 15 pM sample concentration.

    Article Title: Characterization of circulating transfer RNA-derived RNA fragments in cattle
    Article Snippet: After the gel was run the pools were concentrated using the QIAquick PCR purification kit (QIAGEN, Germantown, MD, USA) by eluting in 32 ul of RNase free water. .. One microliter of the size selected library pool was run using a High sensitivity DNA chip Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). .. The concentration was determined by using a 135–170 nucleotide gate.

    Article Title: Pregestational overweight and obesity are associated with differences in gut microbiota composition and systemic inflammation in the third trimester
    Article Snippet: After 16S rDNA gene amplification, the multiplexing step was performed using a Nextera XT Index Kit (Illumina, San Diego, CA, USA). .. One microliter of the PCR product was checked with a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA) and libraries were prepared using a 2x300pb paired-end run (MiSeq Reagent kit v3) according to manufacturer’s instructions (Illumina) at FISABIO sequencing service (Valencia, Spain). .. All clinical data from individual participants were combined according to their pre-BMI in normoweight (N/W), overweight (O/W), and obese (O/O) groups.

    Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
    Article Snippet: All cleaned-up amplicons from the first-step PCR were diluted to 10 ng/μL and added to the second-step PCR reaction mix at a final concentration of 1 ng/μL. .. Thermal cycling conditions were 96°C for 3 min, followed by 8 cycles of 95°C for 30 s, 55°C for 30 s and 72°C for 30 s, with a final extension of 72°C for 5 min. Amplicon sizes (464 bp) of randomly selected sampled were then analyzed by Bioanalyzer DNA 1000 chip (Agilent Technologies). .. The libraries were cleaned-up before quantification using AMPure XP beads (Beckman-Coulter Genomics) following the manufacturer's instructions.

    Article Title: Gut Microbiota Features in Young Children With Autism Spectrum Disorders
    Article Snippet: After each PCR step, amplicons were purified with Agencourt AMPure XP beads (Beckman Coulter Inc.). .. Then, library sizes and concentrations of barcoded amplicons were assessed using Bioanalyzer DNA 1000 chip (Agilent technologies) and Qubit dsDNA BR assay kit (Invitrogen), respectively. .. Normalized libraries were pooled, denatured with NaOH, diluted to 10pM and combined with 25% (v/v) denatured 10pM PhiX, according to Illumina guidelines.

    Article Title: The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog
    Article Snippet: Library construction was performed according to Illumina’s TruSeq small RNA sample prep protocol (Illumina, San Diego CA). .. Library quality was assessed using the Agilent Bioanalyzer DNA chip and quantified using Ribo Green. .. Libraries were subjected to MiSeq analysis to ensure library quality.

    Article Title: The microbiome in PTEN hamartoma tumor syndrome
    Article Snippet: Indexed PCR products were purified with Ampure XP beads (Beckman Coulter, Brea, CA, USA) and quantified with Qubit dsDNA system (ThermoFisher Scientific). .. Samples were then normalized and pooled into sequencing libraries at 20 nM for oral wash and fecal samples and 1 nM for urine samples, then validated on a Bioanalyzer DNA 1000 chip (Agilent) and sequenced on the Illumina MiSeq with a V3 reagent kit at the Case Western Reserve University Genomics Core Facility. .. Paired-end reads, which were 250 bp in length, were merged with FLASH ( ).

    Article Title: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
    Article Snippet: More specifically, whole-genome sequencing libraries were generated from 700 to 1000 ng of genomic DNA spiked with 0.1% (w/w) unmethylated λ DNA (Promega) previously fragmented to 300–400 bp peak sizes using the Covaris focused-ultrasonicator E210. .. Fragment size was controlled on a Bioanalyzer DNA 1000 Chip (Agilent) and the KAPA High Throughput Library Preparation Kit (KAPA Biosystems) was applied. .. End repair of the generated dsDNA with 3′ or 5′ overhangs, adenylation of 3′ ends, adaptor ligation, and clean-up steps were carried out as per KAPA Biosystems’ recommendations.

    Article Title: Neurexins 1–3 Each Have a Distinct Pattern of Expression in the Early Developing Human Cerebral Cortex
    Article Snippet: The concentration of each library was determined using the KAPA quantitative real-time PCR (qPCR) kit (KK4835) and triplicate reactions using three independent 106-fold dilutions of the libraries. .. The size profile of approximately 15% of the libraries was evaluated using an Agilent Bioanalyzer DNA 1000 chip. .. The average final library size was between 272 and 467 bp (includes 120 nucleotides of adapter sequence).

    Article Title: HPV infection and bacterial microbiota in the placenta, uterine cervix and oral mucosa
    Article Snippet: The V3-V4 region of 16S rDNA gene was amplified by PCR using Illumina adapter overhang nucleotide sequences following Illumina protocols. .. After 16S rDNA gene amplification, the multiplexing step was performed using Nextera XT Index Kit (Illumina, San Diego, CA, USA) and PCR product was checked in a Bioanalyzer DNA 1000 chip (Agilent Technologies, Santa Clara, CA, USA). .. Libraries were sequenced using a 2 × 300 pb paired-end run (MiSeq Reagent kit v3) on a MiSeq-Illumina platform (Lifesequencing sequencing service, Valencia, Spain).

    Article Title: Isolation and characterization of human osteoblasts from needle biopsies without in vitro culture
    Article Snippet: Adapter molecules were ligated to the 5′ and 3′ ends of each fragment to facilitate PCR amplification of the fragments to produce the final library. .. The concentration and size distribution of the resulting libraries was determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA). .. The concentration values were confirmed by Qubit fluorometry (Life Technologies, Grand Island, NY).

    Article Title: Loss of eIF4E Phosphorylation Engenders Depression-like Behaviors via Selective mRNA Translation
    Article Snippet: Fragmented mRNA was size-selected on a denaturing 10% polyacrylamide urea gel, and the area corresponding to 35–50 nucleotides was excised, eluted, and precipitated with isopropanol. .. All samples were analyzed on a Bioanalyzer High Sensitivity DNA chip (Agilent Technologies) to confirm expected size range and quantity and sequenced on a HiSeq 2500 system (Illumina). .. Raw sequencing data were demultiplexed by the sequencing facility (Genome Quebec).

    Article Title: Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity
    Article Snippet: The products were purified using the QIAquick PCR Purification Kit (Qiagen) to construct an Illumina paired end library. .. Library quality control was performed with a Bioanalyzer DNA 1000 Chip Series II (Agilent). .. Analysis by qPCR was employed to quantify the libraries before generating the clusters.

    Plasmid Preparation:

    Article Title: Accuracy and quality of massively parallel DNA pyrosequencing
    Article Snippet: We treated each plasmid with plasmid-safe DNAase (Epicentre, Madison, WI, USA) to remove Escherichia coli genomic DNA and confirmed that each plasmid produced an amplification product of the expected size with primers targeting the V6 region of the bacterial rDNA according to Sogin et al . .. We assessed the product quality using a BioAnalyzer Agilent DNA 1000 LabChip following the manufacturer's instructions.

    Software:

    Article Title: Isolation and characterization of human osteoblasts from needle biopsies without in vitro culture
    Article Snippet: The concentration and size distribution of the resulting libraries was determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA). .. Libraries were loaded onto paired end flow cells at concentrations of 8–10 pM to generate cluster densities of 700,000/mm2 following Illumina’s standard protocol using the Illumina cBot and cBot Paired end cluster kit version 3.

    Multiplex Assay:

    Article Title: Isolation and characterization of human osteoblasts from needle biopsies without in vitro culture
    Article Snippet: The concentration and size distribution of the resulting libraries was determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA). .. The concentration values were confirmed by Qubit fluorometry (Life Technologies, Grand Island, NY).

    Selection:

    Article Title: Single-Cell Semiconductor Sequencing
    Article Snippet: Paragraph title: 3.4 Library Size Selection Quality/ Quantity Assessment: Timing 2 h ... Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ).

    Article Title: Characterization of circulating transfer RNA-derived RNA fragments in cattle
    Article Snippet: The pool was then size selected using the Pippin Prep on a 3% Agarose gel without added Ethidium Bromide (SAGE Sciences, Beverly, MA, USA) with a size selection of 142–170 nt according to manufactures instructions. .. One microliter of the size selected library pool was run using a High sensitivity DNA chip Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Sample Prep:

    Article Title: The Rat microRNA body atlas; Evaluation of the microRNA content of rat organs through deep sequencing and characterization of pancreas enriched miRNAs as biomarkers of pancreatic toxicity in the rat and dog
    Article Snippet: Library construction was performed according to Illumina’s TruSeq small RNA sample prep protocol (Illumina, San Diego CA). .. Library quality was assessed using the Agilent Bioanalyzer DNA chip and quantified using Ribo Green.

    Article Title: Neurexins 1–3 Each Have a Distinct Pattern of Expression in the Early Developing Human Cerebral Cortex
    Article Snippet: Briefly, cDNA was generated from the RNAs using Illumina's Stranded mRNA Sample Prep Kit. .. The size profile of approximately 15% of the libraries was evaluated using an Agilent Bioanalyzer DNA 1000 chip.

    Next-Generation Sequencing:

    Article Title: AR intragenic deletions linked to androgen receptor splice variant expression and activity in models of prostate cancer progression
    Article Snippet: Paragraph title: Paired-end library creation, sequence capture, and next-generation sequencing ... A Bioanalyzer DNA 1000 chip (Agilent, Santa Clara, CA) was used to verify DNA samples sheared with fragment peaks between 150-200 bp.

    Spectrophotometry:

    Article Title: Association of prevalent vaginal microbiome of mother with occurrence of type I diabetes in child
    Article Snippet: The DNA was quantified using a Nanodrop spectrophotometer. .. The triplicate pooled PCR amplified reactions were purified using the AMPure XP PCR clean-up kit (Agencourt Bioscience, CA, USA) and the DNA concentration was measured on a Bioanalyzer DNA chip (Agilent Technologies, CA, USA).

    Produced:

    Article Title: Accuracy and quality of massively parallel DNA pyrosequencing
    Article Snippet: We treated each plasmid with plasmid-safe DNAase (Epicentre, Madison, WI, USA) to remove Escherichia coli genomic DNA and confirmed that each plasmid produced an amplification product of the expected size with primers targeting the V6 region of the bacterial rDNA according to Sogin et al . .. We assessed the product quality using a BioAnalyzer Agilent DNA 1000 LabChip following the manufacturer's instructions.

    Concentration Assay:

    Article Title: Single-Cell Semiconductor Sequencing
    Article Snippet: Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ). .. Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ).

    Article Title: Association of prevalent vaginal microbiome of mother with occurrence of type I diabetes in child
    Article Snippet: Triplicate PCR reactions were performed, each containing 1x Phusion GC buffer, 0.4 µM of the forward and reverse primers, 200 µM dNTPs, 0.5 U of Phusion enzyme (Finnzymes, Finland) and 10 ng of genomic community DNA as the template, together with molecular-grade water in a total reaction volume of 20 µl. .. The triplicate pooled PCR amplified reactions were purified using the AMPure XP PCR clean-up kit (Agencourt Bioscience, CA, USA) and the DNA concentration was measured on a Bioanalyzer DNA chip (Agilent Technologies, CA, USA). .. Individual samples were pooled in an equivalent amount, size selected using BluePippin automated electrophoresis system (Sage Science, MA, USA) on 1.5% agarose gel, twice purified with AMPure XP kit, final DNA concentration was measured using Bioanalyzer DNA chip and sequenced on a 316 v2 chip using Ion Torrent 400 bp chemistry (Life Technologies, USA) using to 15 pM sample concentration.

    Article Title: Characterization of circulating transfer RNA-derived RNA fragments in cattle
    Article Snippet: The concentration of each indexed library was determined by using a 135–170 nucleotide gate. .. One microliter of the size selected library pool was run using a High sensitivity DNA chip Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Lab to Field Assessment of the Ecotoxicological Impact of Chlorpyrifos, Isoproturon, or Tebuconazole on the Diversity and Composition of the Soil Bacterial Community
    Article Snippet: All cleaned-up amplicons from the first-step PCR were diluted to 10 ng/μL and added to the second-step PCR reaction mix at a final concentration of 1 ng/μL. .. Thermal cycling conditions were 96°C for 3 min, followed by 8 cycles of 95°C for 30 s, 55°C for 30 s and 72°C for 30 s, with a final extension of 72°C for 5 min. Amplicon sizes (464 bp) of randomly selected sampled were then analyzed by Bioanalyzer DNA 1000 chip (Agilent Technologies).

    Article Title: Neurexins 1–3 Each Have a Distinct Pattern of Expression in the Early Developing Human Cerebral Cortex
    Article Snippet: The concentration of each library was determined using the KAPA quantitative real-time PCR (qPCR) kit (KK4835) and triplicate reactions using three independent 106-fold dilutions of the libraries. .. The size profile of approximately 15% of the libraries was evaluated using an Agilent Bioanalyzer DNA 1000 chip.

    Article Title: Isolation and characterization of human osteoblasts from needle biopsies without in vitro culture
    Article Snippet: Adapter molecules were ligated to the 5′ and 3′ ends of each fragment to facilitate PCR amplification of the fragments to produce the final library. .. The concentration and size distribution of the resulting libraries was determined on an Agilent Bioanalyzer DNA 1000 chip (Santa Clara, CA). .. The concentration values were confirmed by Qubit fluorometry (Life Technologies, Grand Island, NY).

    Fractionation:

    Article Title: Single-Cell Semiconductor Sequencing
    Article Snippet: Fractionation to the appropriate size is performed on an E-Gel® SizeSelect™ 2 % Agarose; see ( see ). .. Band isolations are then run on an Agilent Bioanalyzer™ High Sensitivity DNA chip to assess size and quantity; see ( see ).

    High Throughput Screening Assay:

    Article Title: Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome
    Article Snippet: More specifically, whole-genome sequencing libraries were generated from 700 to 1000 ng of genomic DNA spiked with 0.1% (w/w) unmethylated λ DNA (Promega) previously fragmented to 300–400 bp peak sizes using the Covaris focused-ultrasonicator E210. .. Fragment size was controlled on a Bioanalyzer DNA 1000 Chip (Agilent) and the KAPA High Throughput Library Preparation Kit (KAPA Biosystems) was applied. .. End repair of the generated dsDNA with 3′ or 5′ overhangs, adenylation of 3′ ends, adaptor ligation, and clean-up steps were carried out as per KAPA Biosystems’ recommendations.

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    Agilent technologies bioanalyzer
    Selected <t>bioanalyzer</t> electropherogram overlays from purified DNA (red) or 10% whole blood (blue). Results from five representative donors illustrate examples of a confirmed heterozyote (A) , heterozygote with a 10% blood under the default FU cutoff (B) , and suspected heterozygote with split peaks as an allelic differentiator and a larger artifact (C) , confirmed homozygote (D) , homozygote with two smaller artifacts (E) .
    Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1579 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Selected bioanalyzer electropherogram overlays from purified DNA (red) or 10% whole blood (blue). Results from five representative donors illustrate examples of a confirmed heterozyote (A) , heterozygote with a 10% blood under the default FU cutoff (B) , and suspected heterozygote with split peaks as an allelic differentiator and a larger artifact (C) , confirmed homozygote (D) , homozygote with two smaller artifacts (E) .

    Journal: BMC Medical Genetics

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

    doi: 10.1186/s12881-014-0130-5

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

    Article Snippet: Using the same 15-minute PCR assay with optimized whole blood concentration set at 10%, we increased our sample set to 40 donors to test the reliability of detection methods by using both agarose gels (Figure ) and an Agilent bioanalyzer (Figure ).

    Techniques: Purification

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

    Journal: BMC Medical Genetics

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

    doi: 10.1186/s12881-014-0130-5

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

    Article Snippet: Using the same 15-minute PCR assay with optimized whole blood concentration set at 10%, we increased our sample set to 40 donors to test the reliability of detection methods by using both agarose gels (Figure ) and an Agilent bioanalyzer (Figure ).

    Techniques: Polymerase Chain Reaction, Purification, Marker

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

    Journal: BMC Medical Genetics

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

    doi: 10.1186/s12881-014-0130-5

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

    Article Snippet: Using the same 15-minute PCR assay with optimized whole blood concentration set at 10%, we increased our sample set to 40 donors to test the reliability of detection methods by using both agarose gels (Figure ) and an Agilent bioanalyzer (Figure ).

    Techniques: Purification, Marker

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

    Journal: BMC Medical Genetics

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

    doi: 10.1186/s12881-014-0130-5

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

    Article Snippet: Using the same 15-minute PCR assay with optimized whole blood concentration set at 10%, we increased our sample set to 40 donors to test the reliability of detection methods by using both agarose gels (Figure ) and an Agilent bioanalyzer (Figure ).

    Techniques: Purification

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

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

    Techniques:

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

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

    Techniques:

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

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

    Techniques: