2100 bioanalyzer  (Agilent technologies)

 
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  • 99
    Name:
    2100 Electrophoresis Bioanalyzer Instrument
    Description:

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

    Agilent technologies 2100 bioanalyzer
    Appearance of DNA libraries from Agilent <t>2100</t> <t>Bioanalyzer</t> analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

    https://www.bioz.com/result/2100 bioanalyzer/product/Agilent technologies
    Average 99 stars, based on 4313 article reviews
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    2100 bioanalyzer - by Bioz Stars, 2019-12
    99/100 stars

    Images

    1) Product Images from "Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing"

    Article Title: Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing

    Journal: Standards in Genomic Sciences

    doi: 10.1186/s40793-017-0239-1

    Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)
    Figure Legend Snippet: Appearance of DNA libraries from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of DNA libraries sizes prepared for sequencing with the PacBio SMRTbell 10 kb Template Preparation Kit on the Agilent NGS Workstation. A typical electropherogram using the Agilent bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The DNA libraries and the upper marker co-elutes with each other, the sharper peak is the upper marker, shown in red on the gel image. The average library sizes are: Campylobacter ( green , 9.1 kb), Listeria ( blue , 9.5 kb), Vibrio ( aqua , 10 kb), and Salmonella ( red , 15 kb)

    Techniques Used: Generated, Sequencing, Next-Generation Sequencing, Marker

    Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together
    Figure Legend Snippet: Appearance of sheared DNA from Agilent 2100 Bioanalyzer analysis. Representative electropherogram ( a ) and virtual gel ( b ) are used for visual inspection (generated with the Agilent 2100 Bioanalyzer system with the DNA 12000 Kit) of sheared bacterial genomic DNA with average shearing size for Campylobacter ( green , 10 kb), Listeria ( blue , 13.5 kb), Vibrio ( aqua ,11.6 kb), and Salmonella ( red , 17 kb). Peaks near 35 are the lower marker internal standard for the DNA 12000 kit. A typical electropherogram using the Agilent Bioanalyzer 2100 DNA 12000 kit shows the lower marker at 35 s and the upper marker at 90 s. The sheared DNA and the red upper marker, seen in the gel image, co-elute together

    Techniques Used: Generated, Marker

    2) Product Images from "Reference gene selection for gene expression study in shell gland and spleen of laying hens challenged with infectious bronchitis virus"

    Article Title: Reference gene selection for gene expression study in shell gland and spleen of laying hens challenged with infectious bronchitis virus

    Journal: Scientific Reports

    doi: 10.1038/s41598-017-14693-2

    Amplification of the genes fragments from the shell gland tissue of chicken to assess the specificities of the primers used in the current study. (L) DNA ladder (bp); ( 1 ) 18 S rRNA (63 bp); ( 2 ) ALB (197 bp); ( 3 ) ACTB (139 bp); ( 4 ) GAPDH (66 bp); ( 5 ) HMBS (131 bp); ( 6 ) HPRT1 (245 bp); ( 7 ) RPL4 (235 bp); ( 8 ) SDHA (126 bp); ( 9 ) TBP (147 bp); ( 10 ) YWHAZ (61 bp); ( 11 ) ND4-positive control (137 bp); ( 12 ) TLR7-positive control (200 bp). The upper (purple) and lower (green) markers act as internal standards and are used to align the ladder analysis with the individual DNA sample analysis. The standard curve (plotting migration time against DNA amplicon size), in conjunction with the markers, is then used to calculate DNA fragment sizes for each well from the migration times measured (see Agilent 2100 Bioanalyzer Users Guide for Molecular Assays). The DNA gel in Agilent 2100 Bioanalyzer was performed as per manufacturer’s instructions of Agilent DNA 1000 Kit.
    Figure Legend Snippet: Amplification of the genes fragments from the shell gland tissue of chicken to assess the specificities of the primers used in the current study. (L) DNA ladder (bp); ( 1 ) 18 S rRNA (63 bp); ( 2 ) ALB (197 bp); ( 3 ) ACTB (139 bp); ( 4 ) GAPDH (66 bp); ( 5 ) HMBS (131 bp); ( 6 ) HPRT1 (245 bp); ( 7 ) RPL4 (235 bp); ( 8 ) SDHA (126 bp); ( 9 ) TBP (147 bp); ( 10 ) YWHAZ (61 bp); ( 11 ) ND4-positive control (137 bp); ( 12 ) TLR7-positive control (200 bp). The upper (purple) and lower (green) markers act as internal standards and are used to align the ladder analysis with the individual DNA sample analysis. The standard curve (plotting migration time against DNA amplicon size), in conjunction with the markers, is then used to calculate DNA fragment sizes for each well from the migration times measured (see Agilent 2100 Bioanalyzer Users Guide for Molecular Assays). The DNA gel in Agilent 2100 Bioanalyzer was performed as per manufacturer’s instructions of Agilent DNA 1000 Kit.

    Techniques Used: Amplification, Positive Control, Activated Clotting Time Assay, Migration

    3) Product Images from "Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study"

    Article Title: Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-10-617

    Fingerstick and venipuncture cDNA yields and Agilent 2100 Bioanalyzer traces . The samples included in this figure refer to the same samples as Figure 1. (A) Yields of cDNA post Nugen Ovation amplification of 50 ng total RNA. Yields of cDNA from both fingerstick and venipuncture samples were always above the 4.4 ug cut-off needed to continue with hybridization to GeneChip (B, C, D) Agilent 2100 Bioanalyzer cDNA traces using the NanoChip.
    Figure Legend Snippet: Fingerstick and venipuncture cDNA yields and Agilent 2100 Bioanalyzer traces . The samples included in this figure refer to the same samples as Figure 1. (A) Yields of cDNA post Nugen Ovation amplification of 50 ng total RNA. Yields of cDNA from both fingerstick and venipuncture samples were always above the 4.4 ug cut-off needed to continue with hybridization to GeneChip (B, C, D) Agilent 2100 Bioanalyzer cDNA traces using the NanoChip.

    Techniques Used: Amplification, Hybridization

    Fingerstick and venipuncture RNA yields and Agilent 2100 bioanalyzer traces including RNA integrity numbers (RINs) . (A) Fingerstick starting material: 70 uL, venipuncture starting material: 2.5 mL, yields normalized to 70 uL. (B, C, D) Agilent 2100 Bioanalyzer total RNA traces using the PicoChip (B C) and the NanoChip (D) .
    Figure Legend Snippet: Fingerstick and venipuncture RNA yields and Agilent 2100 bioanalyzer traces including RNA integrity numbers (RINs) . (A) Fingerstick starting material: 70 uL, venipuncture starting material: 2.5 mL, yields normalized to 70 uL. (B, C, D) Agilent 2100 Bioanalyzer total RNA traces using the PicoChip (B C) and the NanoChip (D) .

    Techniques Used:

    4) Product Images from "A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species"

    Article Title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-39946-0

    ( A ) Spotting layout with 3 Biotin marker spots (yellow) rather than the 2 of Fig. 3D . 3 spots of PNA 1 (red) and 3 spots of PNA 2 (blue). ( B ) Agilent Bioanalyzer 2100 gel-like images extrapolated from the capillary electrophoresis for the PCR products of T . cruzi . These gel-like images are produced from the chromatogram of the capillary electrophoresis by the bioanalyzer analysis software. NC: negative control PCR (water); 1–6 PCR reactions using decreasing amounts of gDNA of T. cruzi . 1: 50 ng; 2: 5 ng; 3: 0.5 ng; 4: 0.05 ng; 5: 0.005 ng; 6: 0.0005 ng. ( C ) Decreasing amounts of PCR products were used as templates for the dynamic chemistry reaction to incorporate the SMART-C-Biotin. Positive signals were obtained on both abasic PNA probes with PCR starting concentration from 50 ng up to 0.05 ng (8.7 copies/µL) of template what coincides with the last PCR product that was able to be detected by capillary electrophoresis. A percentage of the relative intensity was calculated using as 100% signal the average of the three biotin marker spots.
    Figure Legend Snippet: ( A ) Spotting layout with 3 Biotin marker spots (yellow) rather than the 2 of Fig. 3D . 3 spots of PNA 1 (red) and 3 spots of PNA 2 (blue). ( B ) Agilent Bioanalyzer 2100 gel-like images extrapolated from the capillary electrophoresis for the PCR products of T . cruzi . These gel-like images are produced from the chromatogram of the capillary electrophoresis by the bioanalyzer analysis software. NC: negative control PCR (water); 1–6 PCR reactions using decreasing amounts of gDNA of T. cruzi . 1: 50 ng; 2: 5 ng; 3: 0.5 ng; 4: 0.05 ng; 5: 0.005 ng; 6: 0.0005 ng. ( C ) Decreasing amounts of PCR products were used as templates for the dynamic chemistry reaction to incorporate the SMART-C-Biotin. Positive signals were obtained on both abasic PNA probes with PCR starting concentration from 50 ng up to 0.05 ng (8.7 copies/µL) of template what coincides with the last PCR product that was able to be detected by capillary electrophoresis. A percentage of the relative intensity was calculated using as 100% signal the average of the three biotin marker spots.

    Techniques Used: Marker, Electrophoresis, Polymerase Chain Reaction, Produced, Software, Negative Control, Concentration Assay

    5) Product Images from "Quantification of Small Non-Coding RNAs Allows an Accurate Comparison of miRNA Expression Profiles"

    Article Title: Quantification of Small Non-Coding RNAs Allows an Accurate Comparison of miRNA Expression Profiles

    Journal: Journal of Biomedicine and Biotechnology

    doi: 10.1155/2009/659028

    Agilent 2100 Bioanalyzer electropherogram profiles of total RNA samples (HeLa cells) extracted with TRIzol reagent (green), MirVana kit (blue), and RNEasy kit (red). Inbox: magnification of small RNA profiles for the three samples (between 23 and 29 seconds).
    Figure Legend Snippet: Agilent 2100 Bioanalyzer electropherogram profiles of total RNA samples (HeLa cells) extracted with TRIzol reagent (green), MirVana kit (blue), and RNEasy kit (red). Inbox: magnification of small RNA profiles for the three samples (between 23 and 29 seconds).

    Techniques Used:

    (a) Gel electrophoresis (polyacrylamide 15% stained with ethidium bromide) of LMW RNA samples (LCL) extracted with TRIzol reagent (lane 1), RNEasy kit (lane 2), and small RNA fraction enriched with MirVana kit (lane 3). LMW profile obtained with MirVana kit extraction is similar to that obtained with TRIzol reagent which is not shown for clarity. (b) Agilent 2100 Bioanalyzer electropherogram profile of LMW RNAs (LCL) extracted with TRIzol (black) superimposed on 5.8S (red), 5S (green), and tRNA (blue) bands eluted from polyacrylamide gel. (c) Lymphoblastoid (LCL) LMW RNA profile obtained after plotting the exported raw data from Agilent electropherogram ( ) together with the PeakFit fitted curve (solid line) and the component peak functions. Seven peaks below the LMW RNA profile were fitted by the software ( r 2 = 0.998693).
    Figure Legend Snippet: (a) Gel electrophoresis (polyacrylamide 15% stained with ethidium bromide) of LMW RNA samples (LCL) extracted with TRIzol reagent (lane 1), RNEasy kit (lane 2), and small RNA fraction enriched with MirVana kit (lane 3). LMW profile obtained with MirVana kit extraction is similar to that obtained with TRIzol reagent which is not shown for clarity. (b) Agilent 2100 Bioanalyzer electropherogram profile of LMW RNAs (LCL) extracted with TRIzol (black) superimposed on 5.8S (red), 5S (green), and tRNA (blue) bands eluted from polyacrylamide gel. (c) Lymphoblastoid (LCL) LMW RNA profile obtained after plotting the exported raw data from Agilent electropherogram ( ) together with the PeakFit fitted curve (solid line) and the component peak functions. Seven peaks below the LMW RNA profile were fitted by the software ( r 2 = 0.998693).

    Techniques Used: Nucleic Acid Electrophoresis, Staining, Software

    6) Product Images from "Delta-Tocotrienol Suppresses Radiation-Induced MicroRNA-30 and Protects Mice and Human CD34+ Cells from Radiation Injury"

    Article Title: Delta-Tocotrienol Suppresses Radiation-Induced MicroRNA-30 and Protects Mice and Human CD34+ Cells from Radiation Injury

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0122258

    DT3 downregulated the expression and secretion of radiation-induced miR-30 in mouse tissues and serum. DT3 or vehicle was administrated 24 h before radiation and mouse tissues and serum were collected 1, 4, 8, or 24 h post-irradiation. (A) RNA and/or miRNA were extracted from mouse cells and serum using mirVana miRNA isolation kits following the manufacturer’s protocol. RNA quality was confirmed with an Agilent 2100 bioanalyzer (Agilent Technologies) with RNA 6000 Nano chips. DT3-treatment completely blocked the radiation-induced miR-30b and miR-30c expressions in mouse (B) BM cells after 7 Gy irradiation and in (C) jejunum and liver cells after 10 Gy irradiation, compared with vehicle-treated mice. (D) DT3-treatment suppressed miR-30b and miR-30c in 7 Gy and 10 Gy irradiated mouse serum at 4, 8, or 24 h post-irradiation. Results were from a total of two experiments, N = 6/group in each experiment; RQ = relative quantitation; * p
    Figure Legend Snippet: DT3 downregulated the expression and secretion of radiation-induced miR-30 in mouse tissues and serum. DT3 or vehicle was administrated 24 h before radiation and mouse tissues and serum were collected 1, 4, 8, or 24 h post-irradiation. (A) RNA and/or miRNA were extracted from mouse cells and serum using mirVana miRNA isolation kits following the manufacturer’s protocol. RNA quality was confirmed with an Agilent 2100 bioanalyzer (Agilent Technologies) with RNA 6000 Nano chips. DT3-treatment completely blocked the radiation-induced miR-30b and miR-30c expressions in mouse (B) BM cells after 7 Gy irradiation and in (C) jejunum and liver cells after 10 Gy irradiation, compared with vehicle-treated mice. (D) DT3-treatment suppressed miR-30b and miR-30c in 7 Gy and 10 Gy irradiated mouse serum at 4, 8, or 24 h post-irradiation. Results were from a total of two experiments, N = 6/group in each experiment; RQ = relative quantitation; * p

    Techniques Used: Expressing, Irradiation, Isolation, Mouse Assay, Quantitation Assay

    7) Product Images from "Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study"

    Article Title: Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-10-617

    Fingerstick and venipuncture cDNA yields and Agilent 2100 Bioanalyzer traces . The samples included in this figure refer to the same samples as Figure 1. (A) Yields of cDNA post Nugen Ovation amplification of 50 ng total RNA. Yields of cDNA from both fingerstick and venipuncture samples were always above the 4.4 ug cut-off needed to continue with hybridization to GeneChip (B, C, D) Agilent 2100 Bioanalyzer cDNA traces using the NanoChip.
    Figure Legend Snippet: Fingerstick and venipuncture cDNA yields and Agilent 2100 Bioanalyzer traces . The samples included in this figure refer to the same samples as Figure 1. (A) Yields of cDNA post Nugen Ovation amplification of 50 ng total RNA. Yields of cDNA from both fingerstick and venipuncture samples were always above the 4.4 ug cut-off needed to continue with hybridization to GeneChip (B, C, D) Agilent 2100 Bioanalyzer cDNA traces using the NanoChip.

    Techniques Used: Amplification, Hybridization

    Fingerstick and venipuncture RNA yields and Agilent 2100 bioanalyzer traces including RNA integrity numbers (RINs) . (A) Fingerstick starting material: 70 uL, venipuncture starting material: 2.5 mL, yields normalized to 70 uL. (B, C, D) Agilent 2100 Bioanalyzer total RNA traces using the PicoChip (B C) and the NanoChip (D) .
    Figure Legend Snippet: Fingerstick and venipuncture RNA yields and Agilent 2100 bioanalyzer traces including RNA integrity numbers (RINs) . (A) Fingerstick starting material: 70 uL, venipuncture starting material: 2.5 mL, yields normalized to 70 uL. (B, C, D) Agilent 2100 Bioanalyzer total RNA traces using the PicoChip (B C) and the NanoChip (D) .

    Techniques Used:

    8) Product Images from "Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens"

    Article Title: Clinical relevance of DNA microarray analyses using archival formalin-fixed paraffin-embedded breast cancer specimens

    Journal: BMC Cancer

    doi: 10.1186/1471-2407-11-253

    Comparison of total RNA and microarray signals between FNAB and FFPE specimens . (A) Comparison of Agilent 2100 Bioanalyzer analysis of total RNA between FNAB and FFPE from a breast cancer sample E(+)H(-)-2. (B) Noise levels of the microarray signals. The average numbers of under-detectable probes from Illumina Human-Ref8 24 K BeadChip are 7906.8 ± 27.9 in 25 FNAB arrays and 9531.4 ± 74.3 in 25 FFPE arrays, respectively. (C) Reproducibility of microarray signal. The averages of Correlation Coefficients are 0.87 ± 0.04 within 25 FNAB arrays, 0.87 ± 0.08 within 25 FFPE arrays, 0.45 ± 0.02 between the 25 FNAB arrays and 25 FFPE arrays, and 0.47 ± 0.02 between the 25 paired FNAB and FFPE arrays, respectively.
    Figure Legend Snippet: Comparison of total RNA and microarray signals between FNAB and FFPE specimens . (A) Comparison of Agilent 2100 Bioanalyzer analysis of total RNA between FNAB and FFPE from a breast cancer sample E(+)H(-)-2. (B) Noise levels of the microarray signals. The average numbers of under-detectable probes from Illumina Human-Ref8 24 K BeadChip are 7906.8 ± 27.9 in 25 FNAB arrays and 9531.4 ± 74.3 in 25 FFPE arrays, respectively. (C) Reproducibility of microarray signal. The averages of Correlation Coefficients are 0.87 ± 0.04 within 25 FNAB arrays, 0.87 ± 0.08 within 25 FFPE arrays, 0.45 ± 0.02 between the 25 FNAB arrays and 25 FFPE arrays, and 0.47 ± 0.02 between the 25 paired FNAB and FFPE arrays, respectively.

    Techniques Used: Microarray, Formalin-fixed Paraffin-Embedded

    9) Product Images from "A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species"

    Article Title: A colorimetric strategy based on dynamic chemistry for direct detection of Trypanosomatid species

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-39946-0

    ( A ) Spotting layout with 3 Biotin marker spots (yellow) rather than the 2 of Fig. 3D . 3 spots of PNA 1 (red) and 3 spots of PNA 2 (blue). ( B ) Agilent Bioanalyzer 2100 gel-like images extrapolated from the capillary electrophoresis for the PCR products of T . cruzi . These gel-like images are produced from the chromatogram of the capillary electrophoresis by the bioanalyzer analysis software. NC: negative control PCR (water); 1–6 PCR reactions using decreasing amounts of gDNA of T. cruzi . 1: 50 ng; 2: 5 ng; 3: 0.5 ng; 4: 0.05 ng; 5: 0.005 ng; 6: 0.0005 ng. ( C ) Decreasing amounts of PCR products were used as templates for the dynamic chemistry reaction to incorporate the SMART-C-Biotin. Positive signals were obtained on both abasic PNA probes with PCR starting concentration from 50 ng up to 0.05 ng (8.7 copies/µL) of template what coincides with the last PCR product that was able to be detected by capillary electrophoresis. A percentage of the relative intensity was calculated using as 100% signal the average of the three biotin marker spots.
    Figure Legend Snippet: ( A ) Spotting layout with 3 Biotin marker spots (yellow) rather than the 2 of Fig. 3D . 3 spots of PNA 1 (red) and 3 spots of PNA 2 (blue). ( B ) Agilent Bioanalyzer 2100 gel-like images extrapolated from the capillary electrophoresis for the PCR products of T . cruzi . These gel-like images are produced from the chromatogram of the capillary electrophoresis by the bioanalyzer analysis software. NC: negative control PCR (water); 1–6 PCR reactions using decreasing amounts of gDNA of T. cruzi . 1: 50 ng; 2: 5 ng; 3: 0.5 ng; 4: 0.05 ng; 5: 0.005 ng; 6: 0.0005 ng. ( C ) Decreasing amounts of PCR products were used as templates for the dynamic chemistry reaction to incorporate the SMART-C-Biotin. Positive signals were obtained on both abasic PNA probes with PCR starting concentration from 50 ng up to 0.05 ng (8.7 copies/µL) of template what coincides with the last PCR product that was able to be detected by capillary electrophoresis. A percentage of the relative intensity was calculated using as 100% signal the average of the three biotin marker spots.

    Techniques Used: Marker, Electrophoresis, Polymerase Chain Reaction, Produced, Software, Negative Control, Concentration Assay

    10) Product Images from "Quantification of Small Non-Coding RNAs Allows an Accurate Comparison of miRNA Expression Profiles"

    Article Title: Quantification of Small Non-Coding RNAs Allows an Accurate Comparison of miRNA Expression Profiles

    Journal: Journal of Biomedicine and Biotechnology

    doi: 10.1155/2009/659028

    Agilent 2100 Bioanalyzer electropherogram profiles of total RNA samples (HeLa cells) extracted with TRIzol reagent (green), MirVana kit (blue), and RNEasy kit (red). Inbox: magnification of small RNA profiles for the three samples (between 23 and 29 seconds).
    Figure Legend Snippet: Agilent 2100 Bioanalyzer electropherogram profiles of total RNA samples (HeLa cells) extracted with TRIzol reagent (green), MirVana kit (blue), and RNEasy kit (red). Inbox: magnification of small RNA profiles for the three samples (between 23 and 29 seconds).

    Techniques Used:

    (a) Gel electrophoresis (polyacrylamide 15% stained with ethidium bromide) of LMW RNA samples (LCL) extracted with TRIzol reagent (lane 1), RNEasy kit (lane 2), and small RNA fraction enriched with MirVana kit (lane 3). LMW profile obtained with MirVana kit extraction is similar to that obtained with TRIzol reagent which is not shown for clarity. (b) Agilent 2100 Bioanalyzer electropherogram profile of LMW RNAs (LCL) extracted with TRIzol (black) superimposed on 5.8S (red), 5S (green), and tRNA (blue) bands eluted from polyacrylamide gel. (c) Lymphoblastoid (LCL) LMW RNA profile obtained after plotting the exported raw data from Agilent electropherogram ( ) together with the PeakFit fitted curve (solid line) and the component peak functions. Seven peaks below the LMW RNA profile were fitted by the software ( r 2 = 0.998693).
    Figure Legend Snippet: (a) Gel electrophoresis (polyacrylamide 15% stained with ethidium bromide) of LMW RNA samples (LCL) extracted with TRIzol reagent (lane 1), RNEasy kit (lane 2), and small RNA fraction enriched with MirVana kit (lane 3). LMW profile obtained with MirVana kit extraction is similar to that obtained with TRIzol reagent which is not shown for clarity. (b) Agilent 2100 Bioanalyzer electropherogram profile of LMW RNAs (LCL) extracted with TRIzol (black) superimposed on 5.8S (red), 5S (green), and tRNA (blue) bands eluted from polyacrylamide gel. (c) Lymphoblastoid (LCL) LMW RNA profile obtained after plotting the exported raw data from Agilent electropherogram ( ) together with the PeakFit fitted curve (solid line) and the component peak functions. Seven peaks below the LMW RNA profile were fitted by the software ( r 2 = 0.998693).

    Techniques Used: Nucleic Acid Electrophoresis, Staining, Software

    11) Product Images from "Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus"

    Article Title: Distribution of ncRNAs expression across hypothalamic-pituitary-gonadal axis in Capra hircus

    Journal: BMC Genomics

    doi: 10.1186/s12864-018-4767-x

    Small RNA libraries preparation. A Agilent 2100 bioanalyzer profile of a small RNA library obtained from RNA extracted from Hypothalamus, Pituitary and Ovary. B Agilent Tape station profile of a small RNA library fraction obtained by size-selection with pippinprep: miRNA libraries (144 bp), ncRNA libraries (198 and 266 bp). In circle sRNA libraries isolated in fraction 1 and fraction 2: a ) 144 bp, b ) 198 bp and ( c ) 266 bp. Illumina adapters were120 bp long
    Figure Legend Snippet: Small RNA libraries preparation. A Agilent 2100 bioanalyzer profile of a small RNA library obtained from RNA extracted from Hypothalamus, Pituitary and Ovary. B Agilent Tape station profile of a small RNA library fraction obtained by size-selection with pippinprep: miRNA libraries (144 bp), ncRNA libraries (198 and 266 bp). In circle sRNA libraries isolated in fraction 1 and fraction 2: a ) 144 bp, b ) 198 bp and ( c ) 266 bp. Illumina adapters were120 bp long

    Techniques Used: Selection, Isolation

    12) Product Images from "Characterization and tissue-specific expression patterns of the Plasmodium chabaudi cir multigene family"

    Article Title: Characterization and tissue-specific expression patterns of the Plasmodium chabaudi cir multigene family

    Journal: Malaria Journal

    doi: 10.1186/1475-2875-10-272

    Transcriptional changes of cir gene expression during the course of infection . For RFLP analyses of expression changes of the cir genes during the course of infection, blood of female NMRI mice infected with 100 pRBCs were passaged on days 7, 14 and 21 days post infections (d.p.i.) into naïve female NMRI mice. Blood of these passaged mice was again collected at 30% parasitaemia. After amplification using the subfamily-specific primers for both subfamilies, 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I and 30 ng were then analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer. The RT-PCR RFLP profiles for four mice of subfamily 1 are presented in (A). The restriction digest of subfamily 2 are shown in the upper panel of (B) where only at day 7 p.i. and day 14 p.i. of mouse 1 a few smaller restriction fragments could be detected. Therefore a second digest with Xap I for 3 h at 37°C was performed (B, lower panel). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker are indicated.
    Figure Legend Snippet: Transcriptional changes of cir gene expression during the course of infection . For RFLP analyses of expression changes of the cir genes during the course of infection, blood of female NMRI mice infected with 100 pRBCs were passaged on days 7, 14 and 21 days post infections (d.p.i.) into naïve female NMRI mice. Blood of these passaged mice was again collected at 30% parasitaemia. After amplification using the subfamily-specific primers for both subfamilies, 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I and 30 ng were then analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer. The RT-PCR RFLP profiles for four mice of subfamily 1 are presented in (A). The restriction digest of subfamily 2 are shown in the upper panel of (B) where only at day 7 p.i. and day 14 p.i. of mouse 1 a few smaller restriction fragments could be detected. Therefore a second digest with Xap I for 3 h at 37°C was performed (B, lower panel). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker are indicated.

    Techniques Used: Expressing, Infection, Mouse Assay, Amplification, Purification, Reverse Transcription Polymerase Chain Reaction, Marker

    Expression profile analyses of cir genes in different tissues of infected mice by RT-PCR RFLP . For RFLP analyses, organs and blood were collected at a parasitaemia of 30% from female NMRI mice infected with 100 pRBCs. After RT-PCR amplification for the six host tissues with the subfamily-specific primers, 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I. The DNA fragments (30 ng) were analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer for accurate sizing. Compared are RT-PCR RFLP profiles of blood, liver, spleen, kidney, lung and brain for four mice for cir subfamily 1 (A) and cir subfamily 2 (B). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker are indicated.
    Figure Legend Snippet: Expression profile analyses of cir genes in different tissues of infected mice by RT-PCR RFLP . For RFLP analyses, organs and blood were collected at a parasitaemia of 30% from female NMRI mice infected with 100 pRBCs. After RT-PCR amplification for the six host tissues with the subfamily-specific primers, 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I. The DNA fragments (30 ng) were analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer for accurate sizing. Compared are RT-PCR RFLP profiles of blood, liver, spleen, kidney, lung and brain for four mice for cir subfamily 1 (A) and cir subfamily 2 (B). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker are indicated.

    Techniques Used: Expressing, Infection, Mouse Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Purification, Marker

    Transcriptional changes of cir genes during intraerythrocytic development . For expression profiling of the cir genes at three different time points in the life cycle, 30 μl tail vein blood of female NMRI mice infected with 100 pRBCs were collected 3 h (early trophozoites), 10 h (late trophozoites) and 17 h (mature trophozoites and early schizonts) after beginning of the light cycle on day 13 p.i. (parasitaemia about 30%). Amplification was performed using the subfamily-specific primers for both subfamilies and 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I and 30 ng were then analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer. The RFLP profiles of subfamily 1 are shown for four mice in (A). The restriction digests of subfamily 2 are shown in the upper panel of (B). Only a few restriction fragments were detected in all samples, therefore RT-PCR products were also restricted with Xap I (B, lower panel). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker were indicated.
    Figure Legend Snippet: Transcriptional changes of cir genes during intraerythrocytic development . For expression profiling of the cir genes at three different time points in the life cycle, 30 μl tail vein blood of female NMRI mice infected with 100 pRBCs were collected 3 h (early trophozoites), 10 h (late trophozoites) and 17 h (mature trophozoites and early schizonts) after beginning of the light cycle on day 13 p.i. (parasitaemia about 30%). Amplification was performed using the subfamily-specific primers for both subfamilies and 150 ng of purified RT-PCR products (approx. 600 bp) were digested with Alu I and 30 ng were then analysed using the DNA 1000 kit for the Agilent 2100 bioanalyzer. The RFLP profiles of subfamily 1 are shown for four mice in (A). The restriction digests of subfamily 2 are shown in the upper panel of (B). Only a few restriction fragments were detected in all samples, therefore RT-PCR products were also restricted with Xap I (B, lower panel). DNA 1000 bp ladder was used and in each lane an upper (1000 bp, purple) and a lower (25 bp, green) marker were indicated.

    Techniques Used: Expressing, Mouse Assay, Infection, Amplification, Purification, Reverse Transcription Polymerase Chain Reaction, Marker

    13) Product Images from "Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival"

    Article Title: Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1002027

    Growth of Nm in human whole blood and RNA analysis. ( A ) Number of bacteria during incubation with human blood. The CFU/ml per single donor is shown during a time course experiment. ( B ) Analysis of isolated total RNA and enriched Nm RNA using a BioAnalyzer 2100 (Agilent). Upper panel: Total RNA collected from Nm incubated in human whole blood, bacterial RNA (shaded arrowheads) and eukaryotic RNA (open arrowheads) are indicated. Lower panel: Enriched bacterial RNA.
    Figure Legend Snippet: Growth of Nm in human whole blood and RNA analysis. ( A ) Number of bacteria during incubation with human blood. The CFU/ml per single donor is shown during a time course experiment. ( B ) Analysis of isolated total RNA and enriched Nm RNA using a BioAnalyzer 2100 (Agilent). Upper panel: Total RNA collected from Nm incubated in human whole blood, bacterial RNA (shaded arrowheads) and eukaryotic RNA (open arrowheads) are indicated. Lower panel: Enriched bacterial RNA.

    Techniques Used: Incubation, Isolation

    14) Product Images from "An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)"

    Article Title: An optimized isolation protocol yields high‐quality RNA from cassava tissues (Manihot esculenta Crantz)

    Journal: FEBS Open Bio

    doi: 10.1002/2211-5463.12561

    Electropherograms of total RNA from cassava obtained using our method showing 18S and 25S rRNA regions with RNA concentrations and RIN values; (A) to (C) correspond with RNA from leaves and storage roots, and (A) and (B) correspond with RNA from different stages of plant development (young and mature leaves). RNA were visualized in denaturing agarose gels stained with SYBR safe. RNA were analyzed using Agilent RNA 6000 Nano Assays in a 2100 Bioanalyzer (Agilent Technologies) and were then used for RNA sequencing.
    Figure Legend Snippet: Electropherograms of total RNA from cassava obtained using our method showing 18S and 25S rRNA regions with RNA concentrations and RIN values; (A) to (C) correspond with RNA from leaves and storage roots, and (A) and (B) correspond with RNA from different stages of plant development (young and mature leaves). RNA were visualized in denaturing agarose gels stained with SYBR safe. RNA were analyzed using Agilent RNA 6000 Nano Assays in a 2100 Bioanalyzer (Agilent Technologies) and were then used for RNA sequencing.

    Techniques Used: Staining, RNA Sequencing Assay

    Electropherogram of sequencing libraries; the graph shows length distribution curves of sequencing libraries obtained using a low‐cost library construction protocol 18 . Curves were generated on a 2100 Bioanalyzer using a DNA 1000 chip (Agilent Technologies). The photograph was provided by Maria Irigoyen and Linda Walling, University of California, Riverside.
    Figure Legend Snippet: Electropherogram of sequencing libraries; the graph shows length distribution curves of sequencing libraries obtained using a low‐cost library construction protocol 18 . Curves were generated on a 2100 Bioanalyzer using a DNA 1000 chip (Agilent Technologies). The photograph was provided by Maria Irigoyen and Linda Walling, University of California, Riverside.

    Techniques Used: Sequencing, Generated, Chromatin Immunoprecipitation

    15) Product Images from "Adaptation of red blood cell lysis represents a fundamental breakthrough that improves the sensitivity of Salmonella detection in blood"

    Article Title: Adaptation of red blood cell lysis represents a fundamental breakthrough that improves the sensitivity of Salmonella detection in blood

    Journal: Journal of Applied Microbiology

    doi: 10.1111/jam.12769

    Microwave lysis of Salmonella . (a) Gold lysing triangles with bowtie configuration and silicone holder in a microwave. (b) Increasing gold cracking with increasing salt concentration (Gold cracking scale 1–5: 1, small cracks; 5, completely cracked). (c) Gold lysing triangle showing extent of cracking when Salmonella is lysed in broth. (d) Gold lysing triangle showing extent of cracking when Salmonella is lysed in blood. (e–f) Fragment size of DNA released from Salmonella lysed in broth and blood, respectively, using an Agilent 2100 Bioanalyzer.
    Figure Legend Snippet: Microwave lysis of Salmonella . (a) Gold lysing triangles with bowtie configuration and silicone holder in a microwave. (b) Increasing gold cracking with increasing salt concentration (Gold cracking scale 1–5: 1, small cracks; 5, completely cracked). (c) Gold lysing triangle showing extent of cracking when Salmonella is lysed in broth. (d) Gold lysing triangle showing extent of cracking when Salmonella is lysed in blood. (e–f) Fragment size of DNA released from Salmonella lysed in broth and blood, respectively, using an Agilent 2100 Bioanalyzer.

    Techniques Used: Lysis, Concentration Assay

    16) Product Images from "Effects of Acute Aerobic Exercise on Rats Serum Extracellular Vesicles Diameter, Concentration and Small RNAs Content"

    Article Title: Effects of Acute Aerobic Exercise on Rats Serum Extracellular Vesicles Diameter, Concentration and Small RNAs Content

    Journal: Frontiers in Physiology

    doi: 10.3389/fphys.2018.00532

    Acute aerobic exercise decreases rat serum EVs modal diameter and increases serum EVs concentration. (A) Workflow representing the acute exercise protocol used to provide aerobic exercise for Wistar rats running on a treadmill. (B) Immunoelectron micrograph of rat serum EVs purified by Exoquick. Black dots are 10 nm gold particle linked to the exosome marker CD63. (C) Tunable resistive pulse sensing (TRPS) analysis showed a slightly reduction in EVs modal diameter in high intensity exercised group compared to non-exercised ( p = 0.057) and moderate intensity exercised groups ( p = 0.028). The median groups for EVs modal diameter range from 88 nm in non-exercised, through 87 nm in low intensity, 91.5 nm in moderate intensity and 85 nm in high intensity exercised group (D) . The concentration of EVs purified from rat’s serum after exercise measured by TRPS. There is a statistical increase in median EVs concentration after exercise, which range from 1.1 × 109 in non-exercised group to 3 × 109 in low intensity exercised group ( p = 0.014), 2.5 × 109 in moderate intensity exercised group ( p = 0.021) and 3 × 109 in high intensity exercised group ( p = 0.02). (E) The median concentration of rat serum EVs proteins. Proteins were purified from EVs and quantified. There is a statistical significance increase in EVs protein concentration median after exercise ranging from 0.935 mg.mL-1 in non-exercised group to 4.33 mg.mL-1 in low intensity exercised group ( p = 0.014), 4.31 mg.mL-1 in moderate intensity exercised group ( p = 0.014) and 4.31 mg.mL-1 in high intensity exercised group ( p = 0.014). (F) Total rat serum protein profile after Exoquick purification analyzed by SDS-PAGE 12%. Exoquick fraction contains EVs proteins while supernatant fraction contains free proteins that were not precipitated by Exoquick. (G) Western blotting of EVs proteins shows an increase in the exosome marker CD63 while increasing the intensity of exercise. ApoA-IV protein levels remained stable regardless of exercise intensity. Calnexin was used to show the absence of endoplasmic reticulum proteins in purified EVs. (H) The concentration of EVs small RNAs from rat’s serum. Small RNAs were purified, quantified and characterized by 2100 Bioanalyzer (Agilent) using a small RNA chip. There is no statistical difference between group medians.
    Figure Legend Snippet: Acute aerobic exercise decreases rat serum EVs modal diameter and increases serum EVs concentration. (A) Workflow representing the acute exercise protocol used to provide aerobic exercise for Wistar rats running on a treadmill. (B) Immunoelectron micrograph of rat serum EVs purified by Exoquick. Black dots are 10 nm gold particle linked to the exosome marker CD63. (C) Tunable resistive pulse sensing (TRPS) analysis showed a slightly reduction in EVs modal diameter in high intensity exercised group compared to non-exercised ( p = 0.057) and moderate intensity exercised groups ( p = 0.028). The median groups for EVs modal diameter range from 88 nm in non-exercised, through 87 nm in low intensity, 91.5 nm in moderate intensity and 85 nm in high intensity exercised group (D) . The concentration of EVs purified from rat’s serum after exercise measured by TRPS. There is a statistical increase in median EVs concentration after exercise, which range from 1.1 × 109 in non-exercised group to 3 × 109 in low intensity exercised group ( p = 0.014), 2.5 × 109 in moderate intensity exercised group ( p = 0.021) and 3 × 109 in high intensity exercised group ( p = 0.02). (E) The median concentration of rat serum EVs proteins. Proteins were purified from EVs and quantified. There is a statistical significance increase in EVs protein concentration median after exercise ranging from 0.935 mg.mL-1 in non-exercised group to 4.33 mg.mL-1 in low intensity exercised group ( p = 0.014), 4.31 mg.mL-1 in moderate intensity exercised group ( p = 0.014) and 4.31 mg.mL-1 in high intensity exercised group ( p = 0.014). (F) Total rat serum protein profile after Exoquick purification analyzed by SDS-PAGE 12%. Exoquick fraction contains EVs proteins while supernatant fraction contains free proteins that were not precipitated by Exoquick. (G) Western blotting of EVs proteins shows an increase in the exosome marker CD63 while increasing the intensity of exercise. ApoA-IV protein levels remained stable regardless of exercise intensity. Calnexin was used to show the absence of endoplasmic reticulum proteins in purified EVs. (H) The concentration of EVs small RNAs from rat’s serum. Small RNAs were purified, quantified and characterized by 2100 Bioanalyzer (Agilent) using a small RNA chip. There is no statistical difference between group medians.

    Techniques Used: Concentration Assay, Purification, Marker, Tunable Resistive Pulse Sensing, Protein Concentration, SDS Page, Western Blot, Chromatin Immunoprecipitation

    17) Product Images from "Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival"

    Article Title: Transcriptome Analysis of Neisseria meningitidis in Human Whole Blood and Mutagenesis Studies Identify Virulence Factors Involved in Blood Survival

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1002027

    Growth of Nm in human whole blood and RNA analysis. ( A ) Number of bacteria during incubation with human blood. The CFU/ml per single donor is shown during a time course experiment. ( B ) Analysis of isolated total RNA and enriched Nm RNA using a BioAnalyzer 2100 (Agilent). Upper panel: Total RNA collected from Nm incubated in human whole blood, bacterial RNA (shaded arrowheads) and eukaryotic RNA (open arrowheads) are indicated. Lower panel: Enriched bacterial RNA.
    Figure Legend Snippet: Growth of Nm in human whole blood and RNA analysis. ( A ) Number of bacteria during incubation with human blood. The CFU/ml per single donor is shown during a time course experiment. ( B ) Analysis of isolated total RNA and enriched Nm RNA using a BioAnalyzer 2100 (Agilent). Upper panel: Total RNA collected from Nm incubated in human whole blood, bacterial RNA (shaded arrowheads) and eukaryotic RNA (open arrowheads) are indicated. Lower panel: Enriched bacterial RNA.

    Techniques Used: Incubation, Isolation

    18) Product Images from "The Effect of Formaldehyde Fixation on RNA"

    Article Title: The Effect of Formaldehyde Fixation on RNA

    Journal:

    doi: 10.1016/j.jmoldx.2011.01.010

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

    Techniques Used:

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

    Techniques Used:

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

    Techniques Used:

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

    Techniques Used:

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

    Techniques Used: Fluorescence

    19) Product Images from "Stage-Regulated GFP Expression in Trypanosoma cruzi: Applications from Host-Parasite Interactions to Drug Screening"

    Article Title: Stage-Regulated GFP Expression in Trypanosoma cruzi: Applications from Host-Parasite Interactions to Drug Screening

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0067441

    Integration of the green fluorescent protein (GFP) gene following parasite transfection. (A) Schematic representation of the pBEX/GFP construct. The expression vector has the Trypanosoma cruzi 18S ribosomal sequences flanking the intergenic regions between the alpha and beta tubulin genes that provides the spliced leader and polyadenylation sites for the GFP mRNA and the neomycin resistance gene (NeoR) used as a selectable marker. (B and C) Southern-blot analyses of transfected parasites. High-molecular weight DNA, isolated from wild-type (WT) epimastigotes of T. cruzi Dm28c (B1 and C1) and Dm28c transfected (T) with pBEX/GFP (fluorescent epimastigotes) (B2 and C2) were separated by PFGE and stained with ethidium bromide. The bands were transferred to nylon membranes and hybridized with [ 32 P]-labeled probes corresponding to the 24S alpha rDNA (B3 and B4), 18S rDNA (C3 and C4) and GFP (B5, B6, C5 and C6) sequences. (D) Total RNA was isolated from wild-type epimastigotes and pBEX fluorescent epimastigotes and analyzed with an Agilent 2100 Bioanalyzer; data are displayed as a densitometry plot (gel-like image). In this analysis, the fluorescent parasites display a rRNA band pattern (D3) similar to that of the wild-type parasites (D2), suggesting that the mobility shift of the 1.4 Mbp chromosome did not affect the production of functional rRNA molecules. D1 = molecular weight marker.
    Figure Legend Snippet: Integration of the green fluorescent protein (GFP) gene following parasite transfection. (A) Schematic representation of the pBEX/GFP construct. The expression vector has the Trypanosoma cruzi 18S ribosomal sequences flanking the intergenic regions between the alpha and beta tubulin genes that provides the spliced leader and polyadenylation sites for the GFP mRNA and the neomycin resistance gene (NeoR) used as a selectable marker. (B and C) Southern-blot analyses of transfected parasites. High-molecular weight DNA, isolated from wild-type (WT) epimastigotes of T. cruzi Dm28c (B1 and C1) and Dm28c transfected (T) with pBEX/GFP (fluorescent epimastigotes) (B2 and C2) were separated by PFGE and stained with ethidium bromide. The bands were transferred to nylon membranes and hybridized with [ 32 P]-labeled probes corresponding to the 24S alpha rDNA (B3 and B4), 18S rDNA (C3 and C4) and GFP (B5, B6, C5 and C6) sequences. (D) Total RNA was isolated from wild-type epimastigotes and pBEX fluorescent epimastigotes and analyzed with an Agilent 2100 Bioanalyzer; data are displayed as a densitometry plot (gel-like image). In this analysis, the fluorescent parasites display a rRNA band pattern (D3) similar to that of the wild-type parasites (D2), suggesting that the mobility shift of the 1.4 Mbp chromosome did not affect the production of functional rRNA molecules. D1 = molecular weight marker.

    Techniques Used: Transfection, Construct, Expressing, Plasmid Preparation, Marker, Southern Blot, Molecular Weight, Isolation, Staining, Labeling, Mobility Shift, Functional Assay

    20) Product Images from "Comprehensive selection of reference genes for quantitative RT-PCR analysis of murine extramedullary hematopoiesis during development"

    Article Title: Comprehensive selection of reference genes for quantitative RT-PCR analysis of murine extramedullary hematopoiesis during development

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0181881

    RNA quality and purity. RNA Integrity Number (RIN) values obtained from Agilent 2100 Bioanalyzer System was utilized to test the quality of the RNA samples and the Histogram of Frequency Distribution of the A260/A280 ratio was used to indicate the purity of the samples. (A) Electrophoresis of representative sample types allows visual inspection of RNA quality of the different tissues (heart, liver, spleen, and thymus). (B) The electropherogram shows 18S (left) and 28S (right) peaks indicative of RNA integrity of the different organs. (C) Histogram of frequency showing the distribution of the purity of RNA was performed using the ratio of absorbance at A260 nm/absorbance at A280 nm. X axis shows the A260/A280 for the 60 samples tested independently.
    Figure Legend Snippet: RNA quality and purity. RNA Integrity Number (RIN) values obtained from Agilent 2100 Bioanalyzer System was utilized to test the quality of the RNA samples and the Histogram of Frequency Distribution of the A260/A280 ratio was used to indicate the purity of the samples. (A) Electrophoresis of representative sample types allows visual inspection of RNA quality of the different tissues (heart, liver, spleen, and thymus). (B) The electropherogram shows 18S (left) and 28S (right) peaks indicative of RNA integrity of the different organs. (C) Histogram of frequency showing the distribution of the purity of RNA was performed using the ratio of absorbance at A260 nm/absorbance at A280 nm. X axis shows the A260/A280 for the 60 samples tested independently.

    Techniques Used: Electrophoresis

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    Incubation:

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

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

    Formalin-fixed Paraffin-Embedded:

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

    Ex Vivo:

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

    RNA Binding Assay:

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

    Flow Cytometry:

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

    Ligation:

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

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

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

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

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

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

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

    Methylation:

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

    Cell Culture:

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

    Generated:

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

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

    DNA HS Assay:

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: The RNA products from the controlled fragmentation step were used to prepare the strand-specific metatranscriptomic library, following the manufacturer’s instruction of Apollo 324 PrepX mRNA library protocol (IntegenX), which is based on directional RNA adaptor ligation. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies). .. Absolute quantitative PCR assay using SYBR FAST ABI Prism QPCR Mast Mix (Kapa Bio Systems) was performed to confirm amplification efficiency and to determine the library loading concentration for sequencing.

    Sequencing:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

    Sonication:

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

    Affinity Purification:

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

    Binding Assay:

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

    Multiplexing:

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

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

    RNA Sequencing Assay:

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

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

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

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

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

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

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

    RNA HS Assay:

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

    Magnetic Beads:

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

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

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

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

    Isolation:

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

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

    Size-exclusion Chromatography:

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

    Purification:

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

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

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

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

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

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

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

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

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

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

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: An Illumina-specific adaptor was sequentially ligated to the 3′ end of cDNA fragments, purified using the AMPure XP beads (Beckman Coulter, Brea, CA, USA), and finally PCR-amplified (13 cycles) using an appropriate indexing primer to allow further samples multiplexing. .. The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA). .. In the presence of adaptor-dimers (Electropherogram’s peak at 100 to 150-bp), another round of magnetic beads purification was performed.

    Article Title: MSTO1 is a cytoplasmic pro‐mitochondrial fusion protein, whose mutation induces myopathy and ataxia in humans
    Article Snippet: First pre‐capture genomic library was prepared using 1 μg of highly purified genomic DNA. .. Crude pre‐captured genomic library was analyzed by Agilent 2100 Bioanalyzer 1000 DNA chip to assess library quality.

    Polymerase Chain Reaction:

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

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

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

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

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

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

    Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
    Article Snippet: Resulting amplicons were purified on a 2 % agarose gel stained with SYBR Safe (Invitrogen, Carlsbad, CA) using the MinElute PCR Purification kit (Qiagen, Valencia, CA). .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA).

    Article Title: Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule
    Article Snippet: An Illumina-specific adaptor was sequentially ligated to the 3′ end of cDNA fragments, purified using the AMPure XP beads (Beckman Coulter, Brea, CA, USA), and finally PCR-amplified (13 cycles) using an appropriate indexing primer to allow further samples multiplexing. .. The PCR-amplified libraries were purified with the AMPure XP beads (Beckman Coulter, Brea, CA, USA) and, then, assessed for their quality and fragments distribution using the 2100 Bioanalyzer DNA 1000 assay (Agilent Technologies, Santa Clara, CA, USA). .. In the presence of adaptor-dimers (Electropherogram’s peak at 100 to 150-bp), another round of magnetic beads purification was performed.

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

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

    Polyacrylamide Gel Electrophoresis:

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

    cDNA Library Assay:

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: Concentration of amplified cDNA was measured using NanoDrop 2000 spectrophotometer. cDNA libraries were then prepared using Ion Plus Fragment library Kit (Ion Torrent, Life Technologies) following manufacturer's protocols. cDNA libraries were purified using Magnetic Bead Cleanup Module (Ion Torrent, Life Technologies). .. The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit). .. In our samples, the amount of short cDNA fragments with length of 25–160 bp did not exceed 10%.

    Agarose Gel Electrophoresis:

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

    Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
    Article Snippet: Resulting amplicons were purified on a 2 % agarose gel stained with SYBR Safe (Invitrogen, Carlsbad, CA) using the MinElute PCR Purification kit (Qiagen, Valencia, CA). .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA).

    Chromatin Immunoprecipitation:

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

    Article Title: Adaptive Changes in the Vestibular System of Land Snail to a 30-Day Spaceflight and Readaptation on Return to Earth
    Article Snippet: Concentration of amplified cDNA was measured using NanoDrop 2000 spectrophotometer. cDNA libraries were then prepared using Ion Plus Fragment library Kit (Ion Torrent, Life Technologies) following manufacturer's protocols. cDNA libraries were purified using Magnetic Bead Cleanup Module (Ion Torrent, Life Technologies). .. The quality of each prepared cDNA library was evaluated using Qubit® 2.0 Fluorometer (with Qubit® dsDNA HS Assay Kit) and Agilent 2100 Bioanalyzer (with High Sensitivity DNA chip and Agilent High Sensitivity DNA Kit). .. In our samples, the amount of short cDNA fragments with length of 25–160 bp did not exceed 10%.

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). .. Libraries were pooled in equimolar quantities and paired-end sequenced on a Rapid Run Mode flowcell with the V3 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

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

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: Briefly, 100–500 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 10 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA). .. Libraries were pooled in equimolar quantities and paired-end sequenced on a Rapid Run Mode flowcell with the V3 sequencing chemistry on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA) following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

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

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

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

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: The RNA products from the controlled fragmentation step were used to prepare the strand-specific metatranscriptomic library, following the manufacturer’s instruction of Apollo 324 PrepX mRNA library protocol (IntegenX), which is based on directional RNA adaptor ligation. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies). .. Absolute quantitative PCR assay using SYBR FAST ABI Prism QPCR Mast Mix (Kapa Bio Systems) was performed to confirm amplification efficiency and to determine the library loading concentration for sequencing.

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

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

    Software:

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

    Real-time Polymerase Chain Reaction:

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

    Article Title: Using Next-Generation Sequencing Transcriptomics To Determine Markers of Post-traumatic Symptoms: Preliminary Findings from a Post-deployment Cohort of Soldiers
    Article Snippet: Briefly, 1000 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented by heat and converted to double stranded cDNA; cDNA was end-repaired and adenylated at the 3′ end to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98° for 30 sec, followed by 15 cycles of 98° for 10 sec, 60° for 30 sec and 72° for 30 sec, and finally an extension step for 5 min at 72°; Each sample was prepared with different indexed adapters to allow for multiplex sequencing. .. One microliter (ul) of the RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems). .. Libraries were pooled in equimolar quantities and paired-end sequenced on a Rapid Run Mode flowcell with the V3 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

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

    Article Title: The duplication mutation of Quebec platelet disorder dysregulates PLAU, but not C10orf55, selectively increasing production of normal PLAU transcripts by megakaryocytes but not granulocytes
    Article Snippet: Briefly, 100–500 ng of total RNA was used as the input material and enriched for poly-A mRNA, fragmented into the 200-300-bases range for 4 minutes at 94°C and converted to double stranded cDNA, end-repaired and adenylated at the 3’ to create an overhang A to allow for ligation of Illumina adapters with an overhang T; library fragments were amplified under the following conditions: initial denaturation at 98°C for 10 seconds, followed by 10 cycles of 98°C for 10 seconds, 60°C for 30 seconds and 72°C for 30 seconds, and finally an extension step for 5 minutes at 72°C; at the amplification step, each sample were amplified with a different barcoded adapters to allow for multiplex sequencing. .. 1 μl of the final RNA libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip (Agilent Technologies) to check for size; RNA libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems, Wilmington, MA). .. Libraries were pooled in equimolar quantities and paired-end sequenced on a Rapid Run Mode flowcell with the V3 sequencing chemistry on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA) following Illumina’s recommended protocol to generate paired-end reads of 100-bases in length.

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

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

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

    Multiplex Assay:

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

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

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

    Selection:

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

    Sample Prep:

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

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

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

    Next-Generation Sequencing:

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

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

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

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

    Random Hexamer Labeling:

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

    Spectrophotometry:

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

    Concentration Assay:

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

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

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

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

    Article Title: An oligotrophic deep-subsurface community dependent on syntrophy is dominated by sulfur-driven autotrophic denitrifiers
    Article Snippet: The RNA products from the controlled fragmentation step were used to prepare the strand-specific metatranscriptomic library, following the manufacturer’s instruction of Apollo 324 PrepX mRNA library protocol (IntegenX), which is based on directional RNA adaptor ligation. .. Library concentration was quantified on Agilent 2100 BioAnalyzer DNA HS chip using Qubit DNA HS assay (Life Technologies). .. Absolute quantitative PCR assay using SYBR FAST ABI Prism QPCR Mast Mix (Kapa Bio Systems) was performed to confirm amplification efficiency and to determine the library loading concentration for sequencing.

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

    DNA Purification:

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

    Standard Deviation:

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

    Staining:

    Article Title: Chemostat culture systems support diverse bacteriophage communities from human feces
    Article Snippet: Resulting amplicons were purified on a 2 % agarose gel stained with SYBR Safe (Invitrogen, Carlsbad, CA) using the MinElute PCR Purification kit (Qiagen, Valencia, CA). .. Amplicons were further purified with Ampure XP beads (Beckman-Coulter, Brea, CA), and molar equivalents were determined for each sample using a Bioanalyzer 2100 HS DNA Kit (Agilent Technologies, Santa Clara, CA).

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    Agilent technologies 2100 bioanalyzer
    Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent <t>2100</t> <t>Bioanalyzer)</t> of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated
    2100 Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 6120 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Postfixation processing of an RNA 50mer with excess formaldehyde removed. Gel-simulated image (Agilent 2100 Bioanalyzer) of the RNA 50mer fixed in 5% buffered formaldehyde (pH 7.4) for 2 hours. A: Lane L: RNA ladder. Lane 1: Non–formaldehyde-treated

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

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

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

    Techniques:

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

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

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

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

    Techniques:

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

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

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

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

    Techniques:

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

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

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

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

    Techniques:

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

    Journal:

    Article Title: The Effect of Formaldehyde Fixation on RNA

    doi: 10.1016/j.jmoldx.2011.01.010

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

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

    Techniques: Fluorescence

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

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

    Techniques:

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

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

    Techniques:

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

    Journal: PLoS ONE

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

    doi: 10.1371/journal.pone.0208508

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

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

    Techniques:

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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-018-5096-9

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

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

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

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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-018-5096-9

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

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

    Techniques: Formalin-fixed Paraffin-Embedded, Positive Control

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

    Journal: BMC Genomics

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

    doi: 10.1186/s12864-018-5096-9

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

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

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