2100 bioanalyzer  (Agilent technologies)

 
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  • 99
    Name:
    2100 Electrophoresis Bioanalyzer Instrument
    Description:

    Catalog Number:
    G2939AA
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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, 2019-08
    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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    Amplification:

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    Mass Spectrometry:

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    Stable Transfection:

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    Expressing:

    Article Title: Blockade of the LRP16-PKR-NF-κB signaling axis sensitizes colorectal carcinoma cells to DNA-damaging cytotoxic therapy
    Article Snippet: Paragraph title: Gene expression microarray data analysis ... The integrity of the RNA was assessed with an Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

    Article Title: DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis
    Article Snippet: The number of biological replicates for each plant genotype were as follows: Col-0 (3 biological replicates), rdd (2), nrpd1 (2), and nrpe1 (2) respectively. .. RNA quality was analyzed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and samples with RNA Integrity Number (RIN) of ≥8.70 were used for the A. thaliana 12 × 135 K gene expression microarray (Nimblegen, Reykjavik, Iceland). .. The 12 × 135 K format allows simultaneously profiling of 12 samples on a single slide.

    Transfection:

    Article Title: Blockade of the LRP16-PKR-NF-κB signaling axis sensitizes colorectal carcinoma cells to DNA-damaging cytotoxic therapy
    Article Snippet: The total RNA from colon cancer cells stably transfected with the control vector or LRP16-expressing plasmid, and treated with or without etoposide (50 μM) for the indicated periods, was isolated and purified with an RNeasy Kit (Qiagen, Hilden, Germany). .. The integrity of the RNA was assessed with an Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

    RAST Test:

    Article Title: Isolation and Characterization of a Shewanella Phage–Host System from the Gut of the Tunicate, Ciona intestinalis
    Article Snippet: The NuGen UltraLow DNA kit was used (Eurofins, Louisville, KY, USA) to prepare libraries, and DNA quality was assessed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), with size selection (400–600 bp) conducted to remove outlier DNA fragments after sonication. .. The NuGen UltraLow DNA kit was used (Eurofins, Louisville, KY, USA) to prepare libraries, and DNA quality was assessed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), with size selection (400–600 bp) conducted to remove outlier DNA fragments after sonication.

    Concentration Assay:

    Article Title: Dynamic Alterations in DNA Methylation Precede Tris(1,3-dichloro-2-propyl)phosphate-Induced Delays in Zebrafish Epiboly
    Article Snippet: Amplicon quality was confirmed using an Agilent 2100 Bioanalyzer system and high-sensitivity DNA kit. .. Amplicon quality was confirmed using an Agilent 2100 Bioanalyzer system and high-sensitivity DNA kit.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. .. After digestion with 0.1 μg μl−1 RNase A (Fermentas, Pittsburgh, PA, USA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY, USA), and pellets were dissolved in H2 O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA, USA).

    Article Title: Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
    Article Snippet: Molarity of each product was measured on a 2100 Bioanalyzer (Agilent Technologies). .. We then calculated the ratios of the log10 transformed NT:IS template molarities, which were regressed against the log10 transformed copy number of known IS concentrations used in each competitive PCR.

    Article Title: Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells
    Article Snippet: Libraries were amplified using KAPA HiFi HotStart polymerase (Kapa Biosystems) for a final 10 cycles. .. Fragment size, purity, and concentration of the libraries were verified using the Agilent Technologies 2100 Bioanalyzer. .. Input and MeDIP raw reads from wild-type and XPC-overexpressing HDFs and pre-iPSCs ( ) were first quality checked with FastQC and aligned onto the human genome (hg19 assembly) using Bowtie , allowing for two mismatches (-n 2) and no multiple alignments (-m 1).

    Article Title: Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests
    Article Snippet: Each sample possessed specific barcode sequences at the front and end of the PCR amplicon to discriminate among each other in the pooled library. .. Both library concentration and exact product size were measured using a KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA, USA) and an Agilent 2100 Bioanalyzer System (Agilent, Santa Clara, CA, USA), respectively. .. A pooled library (20 nM) and a PhiX control v3 (20 nM) (Illumina) were mixed with 0.2 N fresh NaOH and HT1 buffer (Illumina) to produce the final concentration at 12 pM each.

    Article Title: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
    Article Snippet: DNA concentration was measured with Nanodrop 2000 (Thermo Scientific) and Qubit 2.0 Fluorometer (Life Technologies). .. Sample quality was checked in a Bioanalyzer 2100 (Agilent Technologies).

    Article Title: Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases, et al. Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases
    Article Snippet: Amplicons were purified using PCR purification kits following the manufacturer's protocol (NucleoSpin ExtractII; Macherey‐Nagel, Germany). .. We measured the purified DNA concentration and distribution of amplicon length using the Agilent Bioanalyzer 2100 instrument and Agilent DNA 1000 reagent and kit (Agilent Technologies, CA, USA). .. Amplicons were combined based on DNA concentration in equimolar ratios.

    Methylation:

    Article Title: Dynamic Alterations in DNA Methylation Precede Tris(1,3-dichloro-2-propyl)phosphate-Induced Delays in Zebrafish Epiboly
    Article Snippet: These 10 ROIs were selected based on five CpGs that were also impacted by FA within humans , while the remaining five ROIs were selected to represent exonic and intergenic regions with a range of methylation differences relative to vehicle controls. .. Amplicon quality was confirmed using an Agilent 2100 Bioanalyzer system and high-sensitivity DNA kit.

    Cell Culture:

    Article Title: Isolation and Characterization of a Shewanella Phage–Host System from the Gut of the Tunicate, Ciona intestinalis
    Article Snippet: Shewanella fidelis 3313 was cultured in MB overnight at 20 °C with shaking at 90 RPM, and its lytic phage was propagated and purified as described above. .. The NuGen UltraLow DNA kit was used (Eurofins, Louisville, KY, USA) to prepare libraries, and DNA quality was assessed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), with size selection (400–600 bp) conducted to remove outlier DNA fragments after sonication.

    DNA Sequencing:

    Article Title: A Genotypic Analysis of Five P. aeruginosa Strains after Biofilm Infection by Phages Targeting Different Cell Surface Receptors
    Article Snippet: Genomic DNA was sheared by sonication using a Covaris S2 instrument. .. Sizes and concentrations of DNA sequencing libraries were determined on a Bioanalyzer 2100 (DNA1000 chips, Agilent). .. Paired-end sequencing (2 × 50 bp) was performed on one lane on a Hiseq1500 (Illumina) platform using TruSeq PE Cluster KIT v3 – cBot – HS and TruSeq SBS KIT v3 – HS.

    Article Title: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
    Article Snippet: Paragraph title: DNA sequencing ... Sample quality was checked in a Bioanalyzer 2100 (Agilent Technologies).

    Polymerase Chain Reaction:

    Article Title: Dynamic Alterations in DNA Methylation Precede Tris(1,3-dichloro-2-propyl)phosphate-Induced Delays in Zebrafish Epiboly
    Article Snippet: PCR conditions were: 95°C for 10 min, followed by 35 cycles of 95°C for 30 s, 51–65°C (depending on the ROI) for 30 s, and 72°C for 30 s, with a final extension step at 72°C for 7 min. PCR products were cleaned and purified using a QIAquick 96 PCR Purification Kit (Qiagen), and amplicons were quantified using a Qubit 2.0 Fluorometer. .. Amplicon quality was confirmed using an Agilent 2100 Bioanalyzer system and high-sensitivity DNA kit.

    Article Title: Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts
    Article Snippet: The cDNA was purified for normalization using a QIAquick PCR Purification Kit (Qiagen, Hilden, Germany). .. The resulting cDNA was evaluated and quantified using an Agilent DNA 12 000 Kit and Chips on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests
    Article Snippet: Each sample possessed specific barcode sequences at the front and end of the PCR amplicon to discriminate among each other in the pooled library. .. Both library concentration and exact product size were measured using a KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA, USA) and an Agilent 2100 Bioanalyzer System (Agilent, Santa Clara, CA, USA), respectively.

    Article Title: Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films
    Article Snippet: The cycling conditions of the PCR were: one denaturation phase at 94°C for 3 min, followed by 30 phases at 94°C for 45 s, 56°C for 45 s, 72°C for 2 min, and a final extension at 72°C for 7 min. .. The gel-dye mix, marker, PCR products and ladder were loaded to the DNA chip according to the manufacture’s protocol (Agilent DNA 1000 Assay Protocol), next the chip was inserted to the Agilent 2100 Bioanalyzer (Agilent Technologies, Diegem, Belgium) and the chip run was executed. .. The DNA concentration was determined using the Quantifluor dsDNA assay (Promega Corporation, USA).

    Article Title: Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases, et al. Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases
    Article Snippet: Amplicons were purified using PCR purification kits following the manufacturer's protocol (NucleoSpin ExtractII; Macherey‐Nagel, Germany). .. We measured the purified DNA concentration and distribution of amplicon length using the Agilent Bioanalyzer 2100 instrument and Agilent DNA 1000 reagent and kit (Agilent Technologies, CA, USA).

    Sonication:

    Article Title: A Genotypic Analysis of Five P. aeruginosa Strains after Biofilm Infection by Phages Targeting Different Cell Surface Receptors
    Article Snippet: Genomic DNA was sheared by sonication using a Covaris S2 instrument. .. Sizes and concentrations of DNA sequencing libraries were determined on a Bioanalyzer 2100 (DNA1000 chips, Agilent).

    Article Title: Isolation and Characterization of a Shewanella Phage–Host System from the Gut of the Tunicate, Ciona intestinalis
    Article Snippet: Bacterial, phage and prophage DNA were sequenced with the Illumina MiSeq platform generating mate-pair (2 × 250) libraries (Operon, Eurofins MWG Operon LLC, Huntsville, AL, USA). .. The NuGen UltraLow DNA kit was used (Eurofins, Louisville, KY, USA) to prepare libraries, and DNA quality was assessed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), with size selection (400–600 bp) conducted to remove outlier DNA fragments after sonication. .. The resulting mate-pair reads were assembled using approaches described in Deng et al. [ ], first by a de Bruijn graph assembler (Velvet de novo assembler with a k-mer of 35 (phage) and 27 (bacteria) [ ]), followed by the default consensus algorithm in Geneious 8.1.7 (Biomatters Ltd, Auckland, New Zealand) [ ].

    Article Title: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
    Article Snippet: 1.0 µg DNA was sonicated (20 cycles of 30 s at 4°C, low intensity) with Bioruptor Next Generation (Diagenode). .. Sample quality was checked in a Bioanalyzer 2100 (Agilent Technologies).

    Binding Assay:

    Article Title: Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells
    Article Snippet: No sample DNA was recovered for IgG immunoprecipitations, indicating that very little background binding occurred. .. Fragment size, purity, and concentration of the libraries were verified using the Agilent Technologies 2100 Bioanalyzer.

    Methylated DNA Immunoprecipitation:

    Article Title: Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells
    Article Snippet: Paragraph title: MeDIP ... Fragment size, purity, and concentration of the libraries were verified using the Agilent Technologies 2100 Bioanalyzer.

    DNA Extraction:

    Article Title: Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil
    Article Snippet: Paragraph title: 2.1. Genomic DNA extraction and sequencing ... Library quality was evaluated with Agilent 2100 Bioanalyzer.

    Article Title: Isolation and Characterization of a Shewanella Phage–Host System from the Gut of the Tunicate, Ciona intestinalis
    Article Snippet: Paragraph title: 2.3. DNA Extraction, Sequencing and Analysis ... The NuGen UltraLow DNA kit was used (Eurofins, Louisville, KY, USA) to prepare libraries, and DNA quality was assessed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), with size selection (400–600 bp) conducted to remove outlier DNA fragments after sonication.

    Article Title: Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
    Article Snippet: To determine this 1:1 ratio, a set of PCRs with a constant amount of target DNA extraction (25 ng) and a known IS amount were amplified, with the latter serially diluted among reactions. .. Molarity of each product was measured on a 2100 Bioanalyzer (Agilent Technologies).

    Article Title: Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests
    Article Snippet: Paragraph title: DNA extraction and sequencing ... Both library concentration and exact product size were measured using a KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA, USA) and an Agilent 2100 Bioanalyzer System (Agilent, Santa Clara, CA, USA), respectively.

    Article Title: DNA methylation status is more reliable than gene expression at detecting cancer in prostate biopsy
    Article Snippet: Paragraph title: RNA and DNA extraction ... Samples with A260/A280 ratios of 1.8–2.1 were assessed using an Agilent 2100 Bioanalyzer.

    Article Title: Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films
    Article Snippet: Paragraph title: DNA extraction and ARISA PCR ... The gel-dye mix, marker, PCR products and ladder were loaded to the DNA chip according to the manufacture’s protocol (Agilent DNA 1000 Assay Protocol), next the chip was inserted to the Agilent 2100 Bioanalyzer (Agilent Technologies, Diegem, Belgium) and the chip run was executed.

    Nucleic Acid Electrophoresis:

    Article Title: Multiplex detection of nine food-borne pathogens by mPCR and capillary electrophoresis after using a universal pre-enrichment medium
    Article Snippet: Paragraph title: DNA electrophoresis ... Capillary electrophoresis of mPCR reactions products were performed using an Agilent 2100 Bioanalyzer® with DNA 1000® chips.

    Article Title: Plasma Cell-Free DNA Levels Are Elevated in Acute Puumala Hantavirus Infection
    Article Snippet: Extracted cf-DNA samples were analyzed with the High Sensitivity DNA assay kit and an Agilent 2100 Bioanalyzer equipped with Expert 2100 software according to the manufacturer's instructions (Agilent Technologies Inc., Santa Clara, CA). .. Agilent 2100 Bioanalyzer uses a lab-on-a-chip technology to perform gel electrophoresis; nucleic acids are separated analogously to a capillary electrophoresis and normalized to a ladder and two DNA markers, after which the software automatically calculates the size of each band. .. For each plasma sample, the appearance and intensity of low-molecular weight cf-DNA was estimated visually and graded as follows: 1 = no visible cf-DNA or extremely weak band intensity, 2 = intermediate band intensity, 3 = strong band intensity.

    Magnetic Beads:

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. .. After digestion with 0.1 μg μl−1 RNase A (Fermentas, Pittsburgh, PA, USA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY, USA), and pellets were dissolved in H2 O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA, USA). .. MNase-seq libraries were prepared as described (Bioo Scientific, Austin, TX, USA) using 5140-01 NEXTflex DNA Sequencing kit and 514101 NEXTflex DNA Barcodes-6.

    Isolation:

    Article Title: Blockade of the LRP16-PKR-NF-κB signaling axis sensitizes colorectal carcinoma cells to DNA-damaging cytotoxic therapy
    Article Snippet: The total RNA from colon cancer cells stably transfected with the control vector or LRP16-expressing plasmid, and treated with or without etoposide (50 μM) for the indicated periods, was isolated and purified with an RNeasy Kit (Qiagen, Hilden, Germany). .. The integrity of the RNA was assessed with an Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

    Article Title: Pre-Micro RNA Signatures Delineate Stages of Endothelial Cell Transformation in Kaposi Sarcoma
    Article Snippet: Paragraph title: DNA and RNA isolation ... RNA integrity was evaluated using a 2100 Bioanalyzer Series C (Agilent, Santa Clara, CA).

    Article Title: Plasma Cell-Free DNA Levels Are Elevated in Acute Puumala Hantavirus Infection
    Article Snippet: Cf-DNA isolation was performed according to the manufacturer's instructions following the high-sensitivity protocol. .. Agilent 2100 Bioanalyzer uses a lab-on-a-chip technology to perform gel electrophoresis; nucleic acids are separated analogously to a capillary electrophoresis and normalized to a ladder and two DNA markers, after which the software automatically calculates the size of each band.

    Article Title: DNA methylation status is more reliable than gene expression at detecting cancer in prostate biopsy
    Article Snippet: Total RNA and DNA were isolated from surgically resected prostate specimens using the MirVana miRNA Isolation Kit (Ambion, Carlsbad, CA, USA), and the QIAamp DNA Mini Kit (Qiagen), respectively, following manufacturer instructions. .. Samples with A260/A280 ratios of 1.8–2.1 were assessed using an Agilent 2100 Bioanalyzer.

    Flow Cytometry:

    Article Title: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
    Article Snippet: Sample quality was checked in a Bioanalyzer 2100 (Agilent Technologies). .. DNA samples were preconditioned for sequencing by using the TruSeq DNA Sample Preparation Kit (Illumina) and quantified with Step One Plus Real-Time PCR System (Applied Biosystems).

    Purification:

    Article Title: Perturbation of the T cell receptor repertoire occurs with increasing age in dogs
    Article Snippet: 2.2 RNA was purified from EDTA blood using the PureLink™ Total RNA Blood Purification Kit (Promega, Southampton, UK), according to the manufacturer's instructions. .. RNA quality and quantity were assessed using the 2100 Bioanalyzer system (Agilent Technologies, Stockport, UK), where samples with a RIN ≥ 6 were considered of a suitable quality to proceed to complementary DNA synthesis.

    Article Title: Dynamic Alterations in DNA Methylation Precede Tris(1,3-dichloro-2-propyl)phosphate-Induced Delays in Zebrafish Epiboly
    Article Snippet: PCR conditions were: 95°C for 10 min, followed by 35 cycles of 95°C for 30 s, 51–65°C (depending on the ROI) for 30 s, and 72°C for 30 s, with a final extension step at 72°C for 7 min. PCR products were cleaned and purified using a QIAquick 96 PCR Purification Kit (Qiagen), and amplicons were quantified using a Qubit 2.0 Fluorometer. .. Amplicon quality was confirmed using an Agilent 2100 Bioanalyzer system and high-sensitivity DNA kit.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. .. After digestion with 0.1 μg μl−1 RNase A (Fermentas, Pittsburgh, PA, USA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY, USA), and pellets were dissolved in H2 O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA, USA). .. MNase-seq libraries were prepared as described (Bioo Scientific, Austin, TX, USA) using 5140-01 NEXTflex DNA Sequencing kit and 514101 NEXTflex DNA Barcodes-6.

    Article Title: Isolation and Characterization of a Shewanella Phage–Host System from the Gut of the Tunicate, Ciona intestinalis
    Article Snippet: Shewanella fidelis 3313 was cultured in MB overnight at 20 °C with shaking at 90 RPM, and its lytic phage was propagated and purified as described above. .. The NuGen UltraLow DNA kit was used (Eurofins, Louisville, KY, USA) to prepare libraries, and DNA quality was assessed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), with size selection (400–600 bp) conducted to remove outlier DNA fragments after sonication.

    Article Title: Blockade of the LRP16-PKR-NF-κB signaling axis sensitizes colorectal carcinoma cells to DNA-damaging cytotoxic therapy
    Article Snippet: The total RNA from colon cancer cells stably transfected with the control vector or LRP16-expressing plasmid, and treated with or without etoposide (50 μM) for the indicated periods, was isolated and purified with an RNeasy Kit (Qiagen, Hilden, Germany). .. The integrity of the RNA was assessed with an Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

    Article Title: Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts
    Article Snippet: The purified cDNA was precipitated and normalized with a Trimmer-2 cDNA normalization kit (Evrogen, Moscow, Russia). .. The resulting cDNA was evaluated and quantified using an Agilent DNA 12 000 Kit and Chips on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases, et al. Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases
    Article Snippet: Amplicons were purified using PCR purification kits following the manufacturer's protocol (NucleoSpin ExtractII; Macherey‐Nagel, Germany). .. We measured the purified DNA concentration and distribution of amplicon length using the Agilent Bioanalyzer 2100 instrument and Agilent DNA 1000 reagent and kit (Agilent Technologies, CA, USA). .. Amplicons were combined based on DNA concentration in equimolar ratios.

    Sequencing:

    Article Title: A Genotypic Analysis of Five P. aeruginosa Strains after Biofilm Infection by Phages Targeting Different Cell Surface Receptors
    Article Snippet: Paragraph title: Library Preparation and Illumina Sequencing ... Sizes and concentrations of DNA sequencing libraries were determined on a Bioanalyzer 2100 (DNA1000 chips, Agilent).

    Article Title: Dynamic Alterations in DNA Methylation Precede Tris(1,3-dichloro-2-propyl)phosphate-Induced Delays in Zebrafish Epiboly
    Article Snippet: Paragraph title: Bisulfite Amplicon Sequencing (BSAS) ... Amplicon quality was confirmed using an Agilent 2100 Bioanalyzer system and high-sensitivity DNA kit.

    Article Title: Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil
    Article Snippet: Paragraph title: 2.1. Genomic DNA extraction and sequencing ... Library quality was evaluated with Agilent 2100 Bioanalyzer.

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: Paragraph title: Micrococcal nuclease digestion and sequencing (MNase-seq) ... After digestion with 0.1 μg μl−1 RNase A (Fermentas, Pittsburgh, PA, USA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY, USA), and pellets were dissolved in H2 O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA, USA).

    Article Title: Isolation and Characterization of a Shewanella Phage–Host System from the Gut of the Tunicate, Ciona intestinalis
    Article Snippet: Paragraph title: 2.3. DNA Extraction, Sequencing and Analysis ... The NuGen UltraLow DNA kit was used (Eurofins, Louisville, KY, USA) to prepare libraries, and DNA quality was assessed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), with size selection (400–600 bp) conducted to remove outlier DNA fragments after sonication.

    Article Title: Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts
    Article Snippet: The resulting cDNA was evaluated and quantified using an Agilent DNA 12 000 Kit and Chips on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). .. A size selection protocol was applied as smaller cDNAs are more abundant and would otherwise be preferentially sequenced.

    Article Title: Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells
    Article Snippet: Sample DNA was subsequently subjected to another round of size selection to obtain fragment sizes averaging 200–400 bp in length, suitable for sequencing. .. Fragment size, purity, and concentration of the libraries were verified using the Agilent Technologies 2100 Bioanalyzer.

    Article Title: Microbiota in anorexia nervosa: The triangle between bacterial species, metabolites and psychological tests
    Article Snippet: Paragraph title: DNA extraction and sequencing ... Both library concentration and exact product size were measured using a KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA, USA) and an Agilent 2100 Bioanalyzer System (Agilent, Santa Clara, CA, USA), respectively.

    Article Title: Plasmid Flux in Escherichia coli ST131 Sublineages, Analyzed by Plasmid Constellation Network (PLACNET), a New Method for Plasmid Reconstruction from Whole Genome Sequences
    Article Snippet: Sample quality was checked in a Bioanalyzer 2100 (Agilent Technologies). .. Sample quality was checked in a Bioanalyzer 2100 (Agilent Technologies).

    Article Title: Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases, et al. Mosquito vector‐associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod‐borne diseases
    Article Snippet: Additionally, the forward primers contain primer A sequence (5′ CGT ATC GCC TCC CTC GCG CCA TCA G 3′) followed by a ten‐base molecular identifier (MID) sequence tag (Table ), while the reverse primer contained primer B sequence (5′ CTA TGC GCC TTG CCA GCC CGC TCA G 3′) followed by a ten‐base MID tag (Table ). .. We measured the purified DNA concentration and distribution of amplicon length using the Agilent Bioanalyzer 2100 instrument and Agilent DNA 1000 reagent and kit (Agilent Technologies, CA, USA).

    Lab-on-a-Chip:

    Article Title: Plasma Cell-Free DNA Levels Are Elevated in Acute Puumala Hantavirus Infection
    Article Snippet: Extracted cf-DNA samples were analyzed with the High Sensitivity DNA assay kit and an Agilent 2100 Bioanalyzer equipped with Expert 2100 software according to the manufacturer's instructions (Agilent Technologies Inc., Santa Clara, CA). .. Agilent 2100 Bioanalyzer uses a lab-on-a-chip technology to perform gel electrophoresis; nucleic acids are separated analogously to a capillary electrophoresis and normalized to a ladder and two DNA markers, after which the software automatically calculates the size of each band. .. For each plasma sample, the appearance and intensity of low-molecular weight cf-DNA was estimated visually and graded as follows: 1 = no visible cf-DNA or extremely weak band intensity, 2 = intermediate band intensity, 3 = strong band intensity.

    Mouse Assay:

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: For MNase digestion, olfactory neuroepithelia were harvested from Mecp2 WT littermate adult mice and resuspended in PIPES buffer (5 mM PIPES, 85 mM KCl, 0.5% NP-40, pH 8.0) at 4 °C. .. After digestion with 0.1 μg μl−1 RNase A (Fermentas, Pittsburgh, PA, USA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY, USA), and pellets were dissolved in H2 O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA, USA).

    Chromatin Immunoprecipitation:

    Article Title: Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films
    Article Snippet: The cycling conditions of the PCR were: one denaturation phase at 94°C for 3 min, followed by 30 phases at 94°C for 45 s, 56°C for 45 s, 72°C for 2 min, and a final extension at 72°C for 7 min. .. The gel-dye mix, marker, PCR products and ladder were loaded to the DNA chip according to the manufacture’s protocol (Agilent DNA 1000 Assay Protocol), next the chip was inserted to the Agilent 2100 Bioanalyzer (Agilent Technologies, Diegem, Belgium) and the chip run was executed. .. The DNA concentration was determined using the Quantifluor dsDNA assay (Promega Corporation, USA).

    Plasmid Preparation:

    Article Title: Blockade of the LRP16-PKR-NF-κB signaling axis sensitizes colorectal carcinoma cells to DNA-damaging cytotoxic therapy
    Article Snippet: The total RNA from colon cancer cells stably transfected with the control vector or LRP16-expressing plasmid, and treated with or without etoposide (50 μM) for the indicated periods, was isolated and purified with an RNeasy Kit (Qiagen, Hilden, Germany). .. The integrity of the RNA was assessed with an Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

    Software:

    Article Title: Blockade of the LRP16-PKR-NF-κB signaling axis sensitizes colorectal carcinoma cells to DNA-damaging cytotoxic therapy
    Article Snippet: The integrity of the RNA was assessed with an Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). .. The integrity of the RNA was assessed with an Agilent BioAnalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA).

    Article Title: Pre-Micro RNA Signatures Delineate Stages of Endothelial Cell Transformation in Kaposi Sarcoma
    Article Snippet: RNA integrity was evaluated using a 2100 Bioanalyzer Series C (Agilent, Santa Clara, CA). .. RNA integrity was evaluated using a 2100 Bioanalyzer Series C (Agilent, Santa Clara, CA).

    Article Title: Plasma Cell-Free DNA Levels Are Elevated in Acute Puumala Hantavirus Infection
    Article Snippet: Extracted cf-DNA samples were analyzed with the High Sensitivity DNA assay kit and an Agilent 2100 Bioanalyzer equipped with Expert 2100 software according to the manufacturer's instructions (Agilent Technologies Inc., Santa Clara, CA). .. Agilent 2100 Bioanalyzer uses a lab-on-a-chip technology to perform gel electrophoresis; nucleic acids are separated analogously to a capillary electrophoresis and normalized to a ladder and two DNA markers, after which the software automatically calculates the size of each band. .. For each plasma sample, the appearance and intensity of low-molecular weight cf-DNA was estimated visually and graded as follows: 1 = no visible cf-DNA or extremely weak band intensity, 2 = intermediate band intensity, 3 = strong band intensity.

    Selection:

    Article Title: Isolation and Characterization of a Shewanella Phage–Host System from the Gut of the Tunicate, Ciona intestinalis
    Article Snippet: Bacterial, phage and prophage DNA were sequenced with the Illumina MiSeq platform generating mate-pair (2 × 250) libraries (Operon, Eurofins MWG Operon LLC, Huntsville, AL, USA). .. The NuGen UltraLow DNA kit was used (Eurofins, Louisville, KY, USA) to prepare libraries, and DNA quality was assessed on a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA), with size selection (400–600 bp) conducted to remove outlier DNA fragments after sonication. .. The resulting mate-pair reads were assembled using approaches described in Deng et al. [ ], first by a de Bruijn graph assembler (Velvet de novo assembler with a k-mer of 35 (phage) and 27 (bacteria) [ ]), followed by the default consensus algorithm in Geneious 8.1.7 (Biomatters Ltd, Auckland, New Zealand) [ ].

    Article Title: Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts
    Article Snippet: The resulting cDNA was evaluated and quantified using an Agilent DNA 12 000 Kit and Chips on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). .. The resulting cDNA was evaluated and quantified using an Agilent DNA 12 000 Kit and Chips on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Article Title: Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells
    Article Snippet: Sample DNA was subsequently subjected to another round of size selection to obtain fragment sizes averaging 200–400 bp in length, suitable for sequencing. .. Fragment size, purity, and concentration of the libraries were verified using the Agilent Technologies 2100 Bioanalyzer.

    Agarose Gel Electrophoresis:

    Article Title: Draft genome sequence of Trametes villosa (Sw.) Kreisel CCMB561, a tropical white-rot Basidiomycota from the semiarid region of Brazil
    Article Snippet: The quality and quantity of the genomic DNA were assessed by agarose gel electrophoresis and fluorometric analysis, respectively. .. Library quality was evaluated with Agilent 2100 Bioanalyzer.

    Next-Generation Sequencing:

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: After digestion with 0.1 μg μl−1 RNase A (Fermentas, Pittsburgh, PA, USA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY, USA), and pellets were dissolved in H2 O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA, USA). .. MNase-seq libraries were prepared as described (Bioo Scientific, Austin, TX, USA) using 5140-01 NEXTflex DNA Sequencing kit and 514101 NEXTflex DNA Barcodes-6.

    Spectrophotometry:

    Article Title: DNA methylation status is more reliable than gene expression at detecting cancer in prostate biopsy
    Article Snippet: RNA quality and quantity were analysed in a NanoDrop spectrophotometer. .. Samples with A260/A280 ratios of 1.8–2.1 were assessed using an Agilent 2100 Bioanalyzer.

    Produced:

    Article Title: A Genotypic Analysis of Five P. aeruginosa Strains after Biofilm Infection by Phages Targeting Different Cell Surface Receptors
    Article Snippet: DNA sequencing libraries were produced from 1 μg of genomic DNA, following the recommendations of the TruSeq DNA protocol (Illumina). .. Sizes and concentrations of DNA sequencing libraries were determined on a Bioanalyzer 2100 (DNA1000 chips, Agilent).

    Immunoprecipitation:

    Article Title: Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells
    Article Snippet: Following the immunoprecipitation, DNA was recovered by proteinase K treatment and subsequently converted to dsDNA with KAPA HiFi HotStart polymerase (Kapa Biosystems) for four cycles. .. Fragment size, purity, and concentration of the libraries were verified using the Agilent Technologies 2100 Bioanalyzer.

    DNA Purification:

    Article Title: Sequence features accurately predict genome-wide MeCP2 binding in vivo
    Article Snippet: MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. .. After digestion with 0.1 μg μl−1 RNase A (Fermentas, Pittsburgh, PA, USA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY, USA), and pellets were dissolved in H2 O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA, USA). .. MNase-seq libraries were prepared as described (Bioo Scientific, Austin, TX, USA) using 5140-01 NEXTflex DNA Sequencing kit and 514101 NEXTflex DNA Barcodes-6.

    Marker:

    Article Title: Environmental DNA (eDNA) metabarcoding assays to detect invasive invertebrate species in the Great Lakes
    Article Snippet: Molarity of each product was measured on a 2100 Bioanalyzer (Agilent Technologies). .. Molarity of each product was measured on a 2100 Bioanalyzer (Agilent Technologies).

    Article Title: Development of tailored indigenous marine consortia for the degradation of naturally weathered polyethylene films
    Article Snippet: The cycling conditions of the PCR were: one denaturation phase at 94°C for 3 min, followed by 30 phases at 94°C for 45 s, 56°C for 45 s, 72°C for 2 min, and a final extension at 72°C for 7 min. .. The gel-dye mix, marker, PCR products and ladder were loaded to the DNA chip according to the manufacture’s protocol (Agilent DNA 1000 Assay Protocol), next the chip was inserted to the Agilent 2100 Bioanalyzer (Agilent Technologies, Diegem, Belgium) and the chip run was executed. .. The DNA concentration was determined using the Quantifluor dsDNA assay (Promega Corporation, USA).

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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