2100 bioanalyzer  (Agilent technologies)

 
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  • 99
    Name:
    2100 Electrophoresis Bioanalyzer Instrument
    Description:

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

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

    https://www.bioz.com/result/2100 bioanalyzer/product/Agilent technologies
    Average 99 stars, based on 4313 article reviews
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    2100 bioanalyzer - by Bioz Stars, 2019-11
    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

    Related Articles

    DNA Extraction:

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

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

    Centrifugation:

    Article Title: Epigenetic markers in circulating cell‐free DNA as prognostic markers for survival of castration‐resistant prostate cancer patients, et al. Epigenetic markers in circulating cell‐free DNA as prognostic markers for survival of castration‐resistant prostate cancer patients
    Article Snippet: First, a centrifugation step of 16.000g for 10 min was performed to ensure efficient depletion of residual cells, cell debris, and genomic DNA. .. Size and yield of cfDNA was evaluated on a high sensitivity DNA chip of the Agilent 2100 Expert Bioanalyzer (Agilent Technologies Inc. Santa Clara, CA) and with the dsDNA High Sensitivity assay kit on a Qubit 3.0 fluorimeter (Thermo Fisher Scientific, Eugene, OR).

    Amplification:

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

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

    Article Title: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: For PCR analysis, 1.5 μL of cDNA was incubated with 1.25 U of Taq polymerase (Roche Diagnostics), 20 pM primers (reverse primer in exon 24, forward primer in exon 22), and one-time SuperTaq PCR buffer (Enzyme Technologies, UK) and amplified for 30 cycles, each consisting of an incubation for 30 s at 94°C, 30 s at 60°C, and 30 s at 72°C. .. Exon-skipping levels were semiquantitatively determined as the percentages of the total (wild-type and skipped) product with the Agilent 2100 Bioanalyzer (lab-on-a-chip analyzer) as described previously by Spitali et al.

    Article Title: Asthma Induction During Development and Adult Lung Function, Behavior and Brain Gene Expression
    Article Snippet: RNA quantity and quality were determined with a NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 BioAnalyzer™ (Agilent Technologies, Santa Clara, CA, USA), respectively. .. Quantitative real time PCR (qRT-PCR) was conducted to measure relative abundance of the following genes in cDNA: IL-4 (Mm00445259 m1), IL-5 (Mm00439646 m1).

    Article Title: Persistent antigen at vaccination sites induces tumor-specific CD8+ T cell sequestration, dysfunction and deletion
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    Article Snippet: RNA integrity and quality were checked using an Agilent Bioanalyzer 2100. .. RNA integrity and quality were checked using an Agilent Bioanalyzer 2100.

    Synthesized:

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    Article Snippet: In this approach, mRNA was fragmented, cDNA was synthesized, end repaired, and ligated to unique sequencing adaptors to form cDNA libraries. .. Quality control of prepared libraries was made using Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA).

    Picogreen Assay:

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

    Cell Isolation:

    Article Title: The Impact of Self-Identified Race on Epidemiologic Studies of Gene Expression
    Article Snippet: Each clinical center followed a standardized protocol for the technical aspects of sample collection and CD4+ T cell isolation. .. Analysis using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) confirmed average total RNA yields of 2 μg per collection, with no evidence of DNA contamination, minimal evidence of RNA degradation, and 28S:16S ratios of 2.0.

    Quantitative RT-PCR:

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

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

    Electrophoresis:

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

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

    Microarray:

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    Article Title: Gene Transcriptional and Metabolic Profile Changes in Mimetic Aging Mice Induced by D-Galactose
    Article Snippet: The total RNA was quantified using NanoDrop ND-2000 (Thermo Scientific, Wilmington, DE) and the RNA integrity was evaluated using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). .. Next, double- strand cDNA was synthesized using PrimeScript RT reagent Kit (TaKaRa BIO, Shiga, Japan), and then labeled with cyanine-3-CTP.

    Incubation:

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

    Article Title: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: For PCR analysis, 1.5 μL of cDNA was incubated with 1.25 U of Taq polymerase (Roche Diagnostics), 20 pM primers (reverse primer in exon 24, forward primer in exon 22), and one-time SuperTaq PCR buffer (Enzyme Technologies, UK) and amplified for 30 cycles, each consisting of an incubation for 30 s at 94°C, 30 s at 60°C, and 30 s at 72°C. .. Exon-skipping levels were semiquantitatively determined as the percentages of the total (wild-type and skipped) product with the Agilent 2100 Bioanalyzer (lab-on-a-chip analyzer) as described previously by Spitali et al.

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

    Expressing:

    Article Title: PNPLA1 has a crucial role in skin barrier function by directing acylceramide biosynthesis
    Article Snippet: The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies). .. Fluorescently labelled antisense RNA (cRNA targets) were synthesized with a Low Input QuickAmp Labeling Kit according to the manufacturer's protocol (Agilent Technologies).

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

    Article Title: Beclin 1 and autophagy are required for the tumorigenicity of breast cancer stem-like/progenitor cells
    Article Snippet: RNA quality was checked by capillary electrophoresis using the Bioanalyzer 2100 device (Agilent Technologies, Massy, France). .. Previously described PCR primers for the BECN1 gene target were used.

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

    Article Title: The Impact of Self-Identified Race on Epidemiologic Studies of Gene Expression
    Article Snippet: Paragraph title: PERIPHERAL BLOOD CD4+ LYMPHOCYTE EXPRESSION PROFILING ... Analysis using the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) confirmed average total RNA yields of 2 μg per collection, with no evidence of DNA contamination, minimal evidence of RNA degradation, and 28S:16S ratios of 2.0.

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

    Derivative Assay:

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

    Hybridization:

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

    Article Title: Gene Transcriptional and Metabolic Profile Changes in Mimetic Aging Mice Induced by D-Galactose
    Article Snippet: The total RNA was quantified using NanoDrop ND-2000 (Thermo Scientific, Wilmington, DE) and the RNA integrity was evaluated using Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA). .. Next, double- strand cDNA was synthesized using PrimeScript RT reagent Kit (TaKaRa BIO, Shiga, Japan), and then labeled with cyanine-3-CTP.

    Flow Cytometry:

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: We purified PCR products of size comprised between 300 and 800 nt in gel, and analyzed them on the 2100 Bioanalyzer (Agilent) prior to sequencing. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    Lab-on-a-Chip:

    Article Title: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: For PCR analysis, 1.5 μL of cDNA was incubated with 1.25 U of Taq polymerase (Roche Diagnostics), 20 pM primers (reverse primer in exon 24, forward primer in exon 22), and one-time SuperTaq PCR buffer (Enzyme Technologies, UK) and amplified for 30 cycles, each consisting of an incubation for 30 s at 94°C, 30 s at 60°C, and 30 s at 72°C. .. Exon-skipping levels were semiquantitatively determined as the percentages of the total (wild-type and skipped) product with the Agilent 2100 Bioanalyzer (lab-on-a-chip analyzer) as described previously by Spitali et al. .. cDNA was generated in 20 μL reactions, using 1,000 ng of total RNA with random hexamer primers (Roche Diagnostics) and transcriptor reverse transcriptase (Roche Diagnostics) according to the manufacturer’s instructions. ddPCR was performed in duplicate as previously described on 0.5 μL of cDNA using a TaqMan assay spanning the exon 22–23 junction to detect the non-skipped fragment and an assay spanning the exon 22–24 junction to detect the skipped fragment (sequences are listed in ).

    Infection:

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

    Generated:

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

    Article Title: Nucleotide-resolution DNA double-strand breaks mapping by next-generation sequencing
    Article Snippet: We purified PCR products of size comprised between 300 and 800 nt in gel, and analyzed them on the 2100 Bioanalyzer (Agilent) prior to sequencing. .. We assessed library quality and quantity on the 2100 Bioanalyzer (Agilent) using the High Sensitivity DNA Kit (Agilent), and by qPCR with the Kapa Library quantification Kit (KapaBiosystems).

    DNA Sequencing:

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

    Polymerase Chain Reaction:

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

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

    Article Title: Cyclic Peptides to Improve Delivery and Exon Skipping of Antisense Oligonucleotides in a Mouse Model for Duchenne Muscular Dystrophy
    Article Snippet: For PCR analysis, 1.5 μL of cDNA was incubated with 1.25 U of Taq polymerase (Roche Diagnostics), 20 pM primers (reverse primer in exon 24, forward primer in exon 22), and one-time SuperTaq PCR buffer (Enzyme Technologies, UK) and amplified for 30 cycles, each consisting of an incubation for 30 s at 94°C, 30 s at 60°C, and 30 s at 72°C. .. Exon-skipping levels were semiquantitatively determined as the percentages of the total (wild-type and skipped) product with the Agilent 2100 Bioanalyzer (lab-on-a-chip analyzer) as described previously by Spitali et al.

    Article Title: Asthma Induction During Development and Adult Lung Function, Behavior and Brain Gene Expression
    Article Snippet: RNA quantity and quality were determined with a NanoDrop™ spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA) and Agilent 2100 BioAnalyzer™ (Agilent Technologies, Santa Clara, CA, USA), respectively. .. Quantitative real time PCR (qRT-PCR) was conducted to measure relative abundance of the following genes in cDNA: IL-4 (Mm00445259 m1), IL-5 (Mm00439646 m1).

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

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

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

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

    Multiplexing:

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

    Sensitive Assay:

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

    Magnetic Beads:

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

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

    Isolation:

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

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

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

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

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

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

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

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

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

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

    Sequencing:

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

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

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

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

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

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

    RNA Extraction:

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

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

    Labeling:

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

    Purification:

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

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

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

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

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

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

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

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

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

    Reverse Transcription Polymerase Chain Reaction:

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

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

    Lysis:

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

    cDNA Library Assay:

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

    Agarose Gel Electrophoresis:

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

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

    Mouse Assay:

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

    Chromatin Immunoprecipitation:

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

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

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

    Software:

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

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

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

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

    Real-time Polymerase Chain Reaction:

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

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

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

    Multiplex Assay:

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

    Sample Prep:

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

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

    Ethanol Precipitation:

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

    Next-Generation Sequencing:

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

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

    Random Hexamer Labeling:

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

    Spectrophotometry:

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

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

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

    Concentration Assay:

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

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

    High Throughput Screening Assay:

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

    FACS:

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

    Gradient Centrifugation:

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

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

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