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  • 99
    Agilent technologies agilent 2100 bioanalyzer
    Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using <t>Agilent</t> 2100 <t>Bioanalyzer</t> with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.
    Agilent 2100 Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 149319 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Agilent technologies agilent 2100 bioanalyser
    Isolation of cotton tissues from paraffin-embedded sections by laser microdissection (LMD). Isolation of cotton tissues from paraffin-embedded sections by laser microdissection (LMD). Sections before LMD (a, c, e) , and sections after LM (b, d, f) . The area selected for laser microdissection is outlined in green (a region near the damage caused by larvae feeding, which comprised the stamen tissue, viewed at a , c and d ) or blue (a region farther from the injured area, which comprised the carpel tissue, viewed at a , e , and f ). The assessment of extracted RNA integrity from the stamen and carpel are shown in g and h , respectively. Electropherograms were obtained with an <t>Agilent</t> 2100 <t>Bioanalyser.</t> Open and closed arrowheads indicate the 18S and 28S ribosomal RNA peaks, respectively. RNA quality is expressed as the RNA integrity number (RIN). Scale bars = 100 μm.
    Agilent 2100 Bioanalyser, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 8076 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    96
    Agilent technologies bioanalyzer
    GW-COBRA and LA-COBRA library construction results. ( A ) Sonicated genomic DNA isolated from HCT116 cell line (lane 1), 50 ng of Adapter-2 ligated library material (lane 2). Column purified Adapter-2 ligated library material (lane 3); ( B ) PCR amplification test of bisulfite treated library materials. Lane 1, 2, 3 and 4 are produced by 6, 7, 8 and 9 cycles of PCR using GW-A2-FwdP and COBRA-A2-RevP primers from Table 1 with GW-COBRA library material as the template respectively. Lane 5, 6, 7 and 8 are produced by 6, 7, 8 and 9 cycles of PCR using LA-A2+T7-FwdP and COBRA-A2-RevP primers from Table 1 with LA-COBRA library material as the template, respectively; ( C ) Final library products: GW-COBRA and LA-COBRA methylome libraries of HCT116 DNA amplified using flowcell or LADS primer pairs respectively (Lane 2 and 4). Lane 1 and 3 are negative controls for GW-COBRA and LA-COBRA libraries, respectively; ( D ) <t>Bioanalyzer</t> results of GW-COBRA and LA-COBRA methylome sequencing libraries, respectively, prepared from HCT116 cell line DNA. The final library fragments ranged between 150–500 bp with an average size of 257 and 360 bp for GW-COBRA and LA-COBRA, respectively.
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    99
    Agilent technologies bioanalyzer 2100 instrument
    ( a ) Multiplex ligation-dependent genome amplification (MLGA), reaction scheme.  (I)  Genomic DNA is digested by restriction enzyme to generate targets with defined ends.  (II)  Each MLGA probe consists of two oligonucleotides, one selector oligo of 70–74 nt (green) and one general vector oligo of 34 nt (red). MLGA probe together with DNA-ligase forms circular DNA of target molecules after denaturation and hybridization.  (III)  To reduce background signal in the assay, undesirable, linear DNA is degraded by exonuclease I (Exo I).  (IV)  Multiplex PCR is facilitated by using universal primers that hybridize to a sequence in the vector. PCR products are analyzed using the Agilent Bioanalyzer 2100™ electrophoresis system. ( b ) Data from an MLGA set of 14 probes targeting loci on human chromosomes 13, 18, 21, X and Y. The upper graph shows the resulting elution diagrams from analyses of male and female DNA pools.
    Bioanalyzer 2100 Instrument, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 99/100, based on 1577 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Agilent technologies model 2100 bioanalyzer
    ( a ) Multiplex ligation-dependent genome amplification (MLGA), reaction scheme.  (I)  Genomic DNA is digested by restriction enzyme to generate targets with defined ends.  (II)  Each MLGA probe consists of two oligonucleotides, one selector oligo of 70–74 nt (green) and one general vector oligo of 34 nt (red). MLGA probe together with DNA-ligase forms circular DNA of target molecules after denaturation and hybridization.  (III)  To reduce background signal in the assay, undesirable, linear DNA is degraded by exonuclease I (Exo I).  (IV)  Multiplex PCR is facilitated by using universal primers that hybridize to a sequence in the vector. PCR products are analyzed using the Agilent Bioanalyzer 2100™ electrophoresis system. ( b ) Data from an MLGA set of 14 probes targeting loci on human chromosomes 13, 18, 21, X and Y. The upper graph shows the resulting elution diagrams from analyses of male and female DNA pools.
    Model 2100 Bioanalyzer, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 1207 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Agilent technologies rna 6000 nano kit
    ( a ) Multiplex ligation-dependent genome amplification (MLGA), reaction scheme.  (I)  Genomic DNA is digested by restriction enzyme to generate targets with defined ends.  (II)  Each MLGA probe consists of two oligonucleotides, one selector oligo of 70–74 nt (green) and one general vector oligo of 34 nt (red). MLGA probe together with DNA-ligase forms circular DNA of target molecules after denaturation and hybridization.  (III)  To reduce background signal in the assay, undesirable, linear DNA is degraded by exonuclease I (Exo I).  (IV)  Multiplex PCR is facilitated by using universal primers that hybridize to a sequence in the vector. PCR products are analyzed using the Agilent Bioanalyzer 2100™ electrophoresis system. ( b ) Data from an MLGA set of 14 probes targeting loci on human chromosomes 13, 18, 21, X and Y. The upper graph shows the resulting elution diagrams from analyses of male and female DNA pools.
    Rna 6000 Nano Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 92/100, based on 13207 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    Agilent technologies 2100 bioanalyzer platform
    5-Aza-CdR treatment in vivo leads to inhibition of DNMT1 and apoptosis and results in demethylation of tumor suppressor p16INK4A. A. Cell cycle analysis shows that 5-aza-CdR treatment leads to increased apoptosis. Tumor samples were prepared for FACS analysis as described in the methods section and analyzed with a BD FACSCanto II flow cytometer using the BD FACS Diva Software. Values are means ± SEM. Each value is the mean of three replicates for control and 5-aza-CdR day 5 tumors and of two replicates for 5-aza-CdR day 3 tumors. B. DNMT1 is not detected in tumor protein extracts derived from 5-aza-CdR treated mice. Proteins were extracted from tumor tissue from two tumors treated with 5-aza-CdR starting on day 3 and three tumors treated with 5-aza-CdR on day 5 as described in materials and methods. DNMT1 protein levels were analysed by Western Blot. C. Analysis of the p16 INK4A promotor region by COBRA shows demethylation after 5-aza-CdR treatment. DNA was extracted from tumor tissue, bisulfite converted and analysed by COBRA. Restriction fragments were analysed using the Agilent <t>2100</t> <t>Bioanalyzer</t> platform. Normal PBMCs and in vitro by M.SssI methylated PBMCs were used as unmethylated and methylated controls, respectively. Note the re-appearance of the unmethylated fragment in treated samples indicated by the arrow. D. The percentage of methylated fragments is significantly reduced in 5-aza-CdR treated tumors. Percentages of methylated and unmethylated fragments in relation to total peak areas in electropherograms were calculated with Agilent software as described in the methods section.
    2100 Bioanalyzer Platform, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 91/100, based on 784 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Agilent technologies high sensitivity dna kit
    FFAR2 has numerous copies in European broiler and in ancestral chicken genome. <t>qPCR</t> on genomic <t>DNA</t> shows clear difference in ΔCq between FFAR2 genes and the genes carrying only one copy per genome (four genes in European lines and three genes in Ancestral lines). qPCR was performed using “universal” primers able to amplify the 26 sequences of FFAR2 (see supplementary data S1 , Supplementary Material online). FFAR2 error bars indicate standard deviation between two individual chickens. For the single copy genes, error bars represent standard deviation between the Cq measures for the three or four genes from two individual chickens.
    High Sensitivity Dna Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 9014 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    93
    Agilent technologies capillary electrophoresis
    FFAR2 has numerous copies in European broiler and in ancestral chicken genome. <t>qPCR</t> on genomic <t>DNA</t> shows clear difference in ΔCq between FFAR2 genes and the genes carrying only one copy per genome (four genes in European lines and three genes in Ancestral lines). qPCR was performed using “universal” primers able to amplify the 26 sequences of FFAR2 (see supplementary data S1 , Supplementary Material online). FFAR2 error bars indicate standard deviation between two individual chickens. For the single copy genes, error bars represent standard deviation between the Cq measures for the three or four genes from two individual chickens.
    Capillary Electrophoresis, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 1077 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    89
    Agilent technologies 2100 bioanalyzer high sensitivity dna chip
    FFAR2 has numerous copies in European broiler and in ancestral chicken genome. <t>qPCR</t> on genomic <t>DNA</t> shows clear difference in ΔCq between FFAR2 genes and the genes carrying only one copy per genome (four genes in European lines and three genes in Ancestral lines). qPCR was performed using “universal” primers able to amplify the 26 sequences of FFAR2 (see supplementary data S1 , Supplementary Material online). FFAR2 error bars indicate standard deviation between two individual chickens. For the single copy genes, error bars represent standard deviation between the Cq measures for the three or four genes from two individual chickens.
    2100 Bioanalyzer High Sensitivity Dna Chip, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 89/100, based on 359 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94
    Agilent technologies rna 6000 pico kit
    Characterization of exosomal RNA (esRNA) extracted from purified nanovesicles from fresh human aqueous humor. The esRNA was evaluated using Agilent Bioanalyzer 2100 with Agilent <t>RNA</t> 6000 Pico Kit. A) Shows the RNA ladder and B) displays extracted esRNA from one of the human aqueous humor samples. The size of extracted esRNA was less than 200 nucleotides (nt), mostly around 25 nt. C) shows the miRNAs that were identified via small RNA sequencing using Illumina MiSeq sequencing system. The height of each bar indicated the number of sequence reads with perfect match to mature miRNA.
    Rna 6000 Pico Kit, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 94/100, based on 4525 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.

    Journal: BMC Research Notes

    Article Title: Ensuring good quality rna for quantitative real-time pcr isolated from renal proximal tubular cells using laser capture microdissection

    doi: 10.1186/1756-0500-7-62

    Figure Lengend Snippet: Total RNA concentrations from different number of renal cells. Total RNA concentrations were measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit. It was observed that 3000 renal cells yielded a total RNA concentration too low to be detected while 8000 and 18000 renal cells produced similar total RNA yields.

    Article Snippet: RNA integrity number (RIN) RIN was measured using Agilent 2100 Bioanalyzer with Agilent RNA 6000 Pico Kit.

    Techniques: Concentration Assay, Produced

    Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and 2100 Bioanalyzer electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.

    Journal: BMC Research Notes

    Article Title: MicroRNA preparations from individual monogenean Gyrodactylus salaris-a comparison of six commercially available totalRNA extraction kits

    doi: 10.1186/1756-0500-4-217

    Figure Lengend Snippet: Boxplot summary of all data . Semilogarithmic boxplot breakdown of RNA yield for totalRNA, smallRNA and microRNA of all assessed totalRNA extraction kits for 1, 10 and 100 Gyrodactylus salaris specimens. RQI/RIN values of the totalRNA as determined by the instrument software following the Experion and 2100 Bioanalyzer electrophoresis systems are depicted at the bottom. Boxes indicate the 25-75% intervals, squares the mean, and whiskers the standard deviation, where this lies outside the 25-75% interval.

    Article Snippet: The Small RNA Kit (Agilent) was used to analyse smallRNA and miRNA content with the 2100 Bioanalyzer (Agilent).

    Techniques: Software, Electrophoresis, Standard Deviation

    Electropherograms obtained with the Bioanalyzer 2100 in miRNA-Ref and plasma samples. Examples of the profiles obtained from a miRNA-Ref sample at 10 ng/μL ( a , Bio-PicoChip; ( b ), Bio-SmallChip), a miRNA-Ref sample at 1 ng/μL ( c , Bio-PicoChip; ( d ), Bio-SmallChip), and a plasma sample ( e , Bio-PicoChip; ( f ), Bio-SmallChip). The 10 ng/µL miRNA-Ref sample ( a ) was diluted to fit the detection range of the Bio-PicoChip (0.05–5 ng/µL) and the final concentration was calculated by applying the dilution factor to the value obtained by the Bioanalyzer. In the miRNA-Ref samples ( a – d ), the overall profile is consistent with the presence of ribosomic RNA enriched with small RNAs, whereas in plasma samples ( e , f ) only small RNAs, but no long RNAs, are present. All electropherograms include the corresponding quantification (in bold) and the RNA integrity number (RIN) number (in italics) obtained with the Bio-PicoChip ( a , c , e ) or just the quantification (in bold) with the Bio-SmallChip ( b , d , f ).

    Journal: Scientific Reports

    Article Title: Defining quantification methods and optimizing protocols for microarray hybridization of circulating microRNAs

    doi: 10.1038/s41598-017-08134-3

    Figure Lengend Snippet: Electropherograms obtained with the Bioanalyzer 2100 in miRNA-Ref and plasma samples. Examples of the profiles obtained from a miRNA-Ref sample at 10 ng/μL ( a , Bio-PicoChip; ( b ), Bio-SmallChip), a miRNA-Ref sample at 1 ng/μL ( c , Bio-PicoChip; ( d ), Bio-SmallChip), and a plasma sample ( e , Bio-PicoChip; ( f ), Bio-SmallChip). The 10 ng/µL miRNA-Ref sample ( a ) was diluted to fit the detection range of the Bio-PicoChip (0.05–5 ng/µL) and the final concentration was calculated by applying the dilution factor to the value obtained by the Bioanalyzer. In the miRNA-Ref samples ( a – d ), the overall profile is consistent with the presence of ribosomic RNA enriched with small RNAs, whereas in plasma samples ( e , f ) only small RNAs, but no long RNAs, are present. All electropherograms include the corresponding quantification (in bold) and the RNA integrity number (RIN) number (in italics) obtained with the Bio-PicoChip ( a , c , e ) or just the quantification (in bold) with the Bio-SmallChip ( b , d , f ).

    Article Snippet: RNA Integrity The RNA profile and integrity of all samples (inferred by the RIN) was assessed using the Bioanalyzer 2100 (Agilent Technologies) with the Bio-PicoChip and Bio-SmallChip (see Quantification, Agilent 2100 Bioanalyzer).

    Techniques: Concentration Assay

    Electropherogram and “gel-like” image of positive control on the Agilent Bioanalyzer 2100. The x -axis on the electropherogram represents amplicon size (bp), whist the y -axis represents the measurement response of fluorescence units (FUs). Amplicons of interest in order of size (bp) are lower marker (15), Zein (80), Lectin (90), CaMV (108) and combined CaMV 35s promoter/NOS terminator (131) amplicons, and the upper marker (1500).

    Journal: Biotechnology Research International

    Article Title: Applicability of Three Alternative Instruments for Food Authenticity Analysis: GMO Identification

    doi: 10.4061/2011/838232

    Figure Lengend Snippet: Electropherogram and “gel-like” image of positive control on the Agilent Bioanalyzer 2100. The x -axis on the electropherogram represents amplicon size (bp), whist the y -axis represents the measurement response of fluorescence units (FUs). Amplicons of interest in order of size (bp) are lower marker (15), Zein (80), Lectin (90), CaMV (108) and combined CaMV 35s promoter/NOS terminator (131) amplicons, and the upper marker (1500).

    Article Snippet: Many DNA detection and screening protocols that utilise end-point PCR and have been applied on the Agilent Bioanalyzer 2100 have been validated and endorsed by the UK Food Standards Agency (FSA).

    Techniques: Positive Control, Amplification, Fluorescence, Marker

    First-round (unbarcoded) PCR product size composition measurement using microfluidic electrophoresis. The figure plots fragment sizes (calculated based on migration times relative to those of standards) and fluorescence intensity (FU) of first-round PCR products (see cycling conditions in Methods or Supplementary Fig. 2 legend) measured with the Agilent Bioanalyzer 2100 System. The first peak represents primer polymerization that is removed in subsequent gel excision/re-solubilization steps. The second peak matches expectations for the multi-target GLST product (164 – 204 bp). Special thanks to Craig Lapsley at the Wellcome Centre for Molecular Parasitology in Glasgow for generating this data.

    Journal: bioRxiv

    Article Title: Genome-wide locus sequence typing (GLST) of eukaryotic pathogens

    doi: 10.1101/2020.03.24.003590

    Figure Lengend Snippet: First-round (unbarcoded) PCR product size composition measurement using microfluidic electrophoresis. The figure plots fragment sizes (calculated based on migration times relative to those of standards) and fluorescence intensity (FU) of first-round PCR products (see cycling conditions in Methods or Supplementary Fig. 2 legend) measured with the Agilent Bioanalyzer 2100 System. The first peak represents primer polymerization that is removed in subsequent gel excision/re-solubilization steps. The second peak matches expectations for the multi-target GLST product (164 – 204 bp). Special thanks to Craig Lapsley at the Wellcome Centre for Molecular Parasitology in Glasgow for generating this data.

    Article Snippet: First-round PCR products were electrophoresed in 0.8% agarose gel to separate target bands (mode =164 nt) from primer polymers quantified with the Agilent Bioanalyzer 2100 System (see 78 nt primer peak in ).

    Techniques: Polymerase Chain Reaction, Electrophoresis, Migration, Fluorescence

    Final (barcoded) GLST pool size composition measurement using microfluidic electrophoresis. The figure plots fragment sizes (calculated based on migration times relative to those of standards) and fluorescence intensity (FU) of the final GLST pool measured with the Agilent Bioanalyzer 2100 System. The large peak matches expectations for the multi-target GLST product pool (224 – 264 bp). Left and right peaks labelled in green and purple represent standards of known size. A small non-target peak remaining near 151 bp encourages improvement of prior size selection steps. Special thanks to Julie Galbraith at Glasgow Polyomics for generating this data.

    Journal: bioRxiv

    Article Title: Genome-wide locus sequence typing (GLST) of eukaryotic pathogens

    doi: 10.1101/2020.03.24.003590

    Figure Lengend Snippet: Final (barcoded) GLST pool size composition measurement using microfluidic electrophoresis. The figure plots fragment sizes (calculated based on migration times relative to those of standards) and fluorescence intensity (FU) of the final GLST pool measured with the Agilent Bioanalyzer 2100 System. The large peak matches expectations for the multi-target GLST product pool (224 – 264 bp). Left and right peaks labelled in green and purple represent standards of known size. A small non-target peak remaining near 151 bp encourages improvement of prior size selection steps. Special thanks to Julie Galbraith at Glasgow Polyomics for generating this data.

    Article Snippet: First-round PCR products were electrophoresed in 0.8% agarose gel to separate target bands (mode =164 nt) from primer polymers quantified with the Agilent Bioanalyzer 2100 System (see 78 nt primer peak in ).

    Techniques: Electrophoresis, Migration, Fluorescence, Selection

    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)

    Journal: Standards in Genomic Sciences

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

    doi: 10.1186/s40793-017-0239-1

    Figure Lengend 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)

    Article Snippet: We will discuss the automation of preparation of libraries with the SMRTbell Template Preparation kit as well as analysis of gDNA, fragmented DNA and the final libraries ready for sequencing with both the Agilent electrophoresis platform: Agilent 2100 Bioanalyzer System using the DNA 12000 assay and the Agilent TapeStation System using the genomic DNA ScreenTape and matching reagents.

    Techniques: 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

    Journal: Standards in Genomic Sciences

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

    doi: 10.1186/s40793-017-0239-1

    Figure Lengend 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

    Article Snippet: We will discuss the automation of preparation of libraries with the SMRTbell Template Preparation kit as well as analysis of gDNA, fragmented DNA and the final libraries ready for sequencing with both the Agilent electrophoresis platform: Agilent 2100 Bioanalyzer System using the DNA 12000 assay and the Agilent TapeStation System using the genomic DNA ScreenTape and matching reagents.

    Techniques: Generated, Marker

    FANCI functions in LSU pre-rRNA processing. ( A ). The 41S, 32S, and 12S pre-rRNAs are detected by a probe (P5) that hybridizes with ITS2. ( B ) FANCI depletion results in LSU pre-rRNA processing defects. HeLa cells were transfected with the indicated siRNAs, and total RNA was harvested after 72 h of depletion. Pre-rRNAs were separated by gel electrophoresis, and Northern blots were performed using radioactively labeled P5 probe. Northern blotting with a probe against the 7SL RNA was used as a loading control. Small illustrations of the pre-rRNAs are to the right of their respective bands. ( C – I ) profiles for Northern blotting from three biological replicates for mock ( C ), siFANCI-pool ( D ), siFANCI-2 ( E ), siFANCI-3 ( F ), siPES1 ( G ), siNOL11 ( H ), and siFANCD2 ( I ). Statistical significance was calculated using a two-way ANOVA with Sidak multiple comparisons test (mean ± SD). All comparisons are relative to siNT. The x axes of all graphs were equalized, except for siPES1 in G , which has larger RAMP values. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, **** P ≤ 0.0001. Unmarked bars are not significant. ( J ) FANCI depletion results in decreased mature 28S rRNA relative to 18S. The ratio of 28S/18S was calculated using an Agilent 2100 Bioanalyzer. Statistical significance was calculated using a one-tailed unpaired Mann–Whitney U test for three biological replicates (mean ± SD). All comparisons are relative to siNT.

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    Article Title: Fanconi anemia protein FANCI functions in ribosome biogenesis

    doi: 10.1073/pnas.1811557116

    Figure Lengend Snippet: FANCI functions in LSU pre-rRNA processing. ( A ). The 41S, 32S, and 12S pre-rRNAs are detected by a probe (P5) that hybridizes with ITS2. ( B ) FANCI depletion results in LSU pre-rRNA processing defects. HeLa cells were transfected with the indicated siRNAs, and total RNA was harvested after 72 h of depletion. Pre-rRNAs were separated by gel electrophoresis, and Northern blots were performed using radioactively labeled P5 probe. Northern blotting with a probe against the 7SL RNA was used as a loading control. Small illustrations of the pre-rRNAs are to the right of their respective bands. ( C – I ) profiles for Northern blotting from three biological replicates for mock ( C ), siFANCI-pool ( D ), siFANCI-2 ( E ), siFANCI-3 ( F ), siPES1 ( G ), siNOL11 ( H ), and siFANCD2 ( I ). Statistical significance was calculated using a two-way ANOVA with Sidak multiple comparisons test (mean ± SD). All comparisons are relative to siNT. The x axes of all graphs were equalized, except for siPES1 in G , which has larger RAMP values. * P ≤ 0.05, ** P ≤ 0.01, *** P ≤ 0.001, **** P ≤ 0.0001. Unmarked bars are not significant. ( J ) FANCI depletion results in decreased mature 28S rRNA relative to 18S. The ratio of 28S/18S was calculated using an Agilent 2100 Bioanalyzer. Statistical significance was calculated using a one-tailed unpaired Mann–Whitney U test for three biological replicates (mean ± SD). All comparisons are relative to siNT.

    Article Snippet: To measure the ratio of mature 28S to 18S rRNAs, total RNA that was prepared as described above was run on an Agilent Technologies 2100 Bioanalyzer at the Yale Center for Genome Analysis.

    Techniques: Transfection, Nucleic Acid Electrophoresis, Northern Blot, Labeling, One-tailed Test, MANN-WHITNEY

    Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000

    Journal: Analytical and bioanalytical chemistry

    Article Title: Extraction of microRNAs from biological matrices with titanium dioxide nanofibers

    doi: 10.1007/s00216-017-0649-3

    Figure Lengend Snippet: Comparison of small RNA extraction from MDA-MB-231 cells with fibers and columns analyzed by an Agilent 2100 Bioanalyzer. Small RNA recovery was as high as 985 pg/μL with the fibers and 10.2 pg/μL with the columns from as little as 134,000

    Article Snippet: The chip was run on an Agilent 2100 Bioanalyzer Instrument using the Small RNA Analysis Kit with 1 μL of extraction sample following the protocol provided by Agilent.

    Techniques: RNA Extraction, Multiple Displacement Amplification

    Absence of gnd gene in S. bongori strains . The gnd gene was PCR-amplified as described in the Materials and Methods from eight different strains of S. bongori . PCR products were resolved using the Agilent 7500 DNA kit and the Agilent 2100 Bioanalyzer. Negative Control 1 corresponds to PCR reagents mix + water as a template; and Negative Control 2 corresponds to DNA from a known gnd negative bacterial strain using our PCR conditions.

    Journal: Frontiers in Microbiology

    Article Title: Differentiation of Salmonella strains from the SARA, SARB and SARC reference collections by using three genes PCR-RFLP and the 2100 Agilent Bioanalyzer

    doi: 10.3389/fmicb.2014.00417

    Figure Lengend Snippet: Absence of gnd gene in S. bongori strains . The gnd gene was PCR-amplified as described in the Materials and Methods from eight different strains of S. bongori . PCR products were resolved using the Agilent 7500 DNA kit and the Agilent 2100 Bioanalyzer. Negative Control 1 corresponds to PCR reagents mix + water as a template; and Negative Control 2 corresponds to DNA from a known gnd negative bacterial strain using our PCR conditions.

    Article Snippet: Previous studies have demonstrated improved accuracy and reproducibility of RFLP using the 2100 Agilent Bioanalyzer for the sizing of the DNA fragments (Panaro et al., ; Nachamkin et al., ; Lu et al., ; Hathaway et al., ).

    Techniques: Polymerase Chain Reaction, Amplification, Negative Control

    Isolation of cotton tissues from paraffin-embedded sections by laser microdissection (LMD). Isolation of cotton tissues from paraffin-embedded sections by laser microdissection (LMD). Sections before LMD (a, c, e) , and sections after LM (b, d, f) . The area selected for laser microdissection is outlined in green (a region near the damage caused by larvae feeding, which comprised the stamen tissue, viewed at a , c and d ) or blue (a region farther from the injured area, which comprised the carpel tissue, viewed at a , e , and f ). The assessment of extracted RNA integrity from the stamen and carpel are shown in g and h , respectively. Electropherograms were obtained with an Agilent 2100 Bioanalyser. Open and closed arrowheads indicate the 18S and 28S ribosomal RNA peaks, respectively. RNA quality is expressed as the RNA integrity number (RIN). Scale bars = 100 μm.

    Journal: BMC Genomics

    Article Title: Transcriptome analysis of Gossypium hirsutum flower buds infested by cotton boll weevil (Anthonomus grandis) larvae

    doi: 10.1186/1471-2164-15-854

    Figure Lengend Snippet: Isolation of cotton tissues from paraffin-embedded sections by laser microdissection (LMD). Isolation of cotton tissues from paraffin-embedded sections by laser microdissection (LMD). Sections before LMD (a, c, e) , and sections after LM (b, d, f) . The area selected for laser microdissection is outlined in green (a region near the damage caused by larvae feeding, which comprised the stamen tissue, viewed at a , c and d ) or blue (a region farther from the injured area, which comprised the carpel tissue, viewed at a , e , and f ). The assessment of extracted RNA integrity from the stamen and carpel are shown in g and h , respectively. Electropherograms were obtained with an Agilent 2100 Bioanalyser. Open and closed arrowheads indicate the 18S and 28S ribosomal RNA peaks, respectively. RNA quality is expressed as the RNA integrity number (RIN). Scale bars = 100 μm.

    Article Snippet: The quality of total RNA extracted from LMD-collected tissues was assessed using an RNA 6000 Pico kit on the Agilent 2100 Bioanalyser (Agilent Technologies).

    Techniques: Isolation, Laser Capture Microdissection

    Quality of root-extracted RNA. The analysis of the total RNA extracted from inoculated roots was performed using an Agilent Bioanalyser 2100. One microlitre of RQ1 DNase-treated total RNA was analysed for each sample. The days post-inoculation with  Gaeumannomyces graminis  var.  tritici  ( Ggt ) are indicated. M, RNA size marker; lanes 1, 3, 6, 9, RNA from uninfected wheat roots; lanes 2, 4, 7, 10, RNA from wheat roots infected with  Ggt ; lanes 5, 8, 11, RNA from wheat roots infected with  Ggt  and Pf29Arp; lane 12, RNA from soil-borne pathogenic fungus IV-26/00.

    Journal: Molecular Plant Pathology

    Article Title: The biocontrol bacterium Pseudomonas fluorescens Pf29Arp strain affects the pathogenesis-related gene expression of the take-all fungus Gaeumannomyces graminis var. tritici on wheat roots

    doi: 10.1111/j.1364-3703.2011.00715.x

    Figure Lengend Snippet: Quality of root-extracted RNA. The analysis of the total RNA extracted from inoculated roots was performed using an Agilent Bioanalyser 2100. One microlitre of RQ1 DNase-treated total RNA was analysed for each sample. The days post-inoculation with Gaeumannomyces graminis var. tritici ( Ggt ) are indicated. M, RNA size marker; lanes 1, 3, 6, 9, RNA from uninfected wheat roots; lanes 2, 4, 7, 10, RNA from wheat roots infected with Ggt ; lanes 5, 8, 11, RNA from wheat roots infected with Ggt and Pf29Arp; lane 12, RNA from soil-borne pathogenic fungus IV-26/00.

    Article Snippet: RNA purity and quality were assessed with a Bioanalyser 2100 (Agilent) and quantified with a Nanodrop (Agilent).

    Techniques: Marker, Infection

    Agilent BioAnalyser 2100 traces of total RNA samples. Different volumes of peripheral blood were processed using PAXgene reagent as described in the text. A) Full scale 2.5 mL peripheral blood extraction B) 1.0 mL peripheral blood scaled down extraction C) 0.3 mL peripheral blood scaled down extraction D) Stratagene Universal RNA. The 2.5 mL and 1.0 mL extractions were run on eukaryote total RNA Nano chips and the 0.3 mL extractions and the Universal RNA shown were run on Pico chips. The 18s and 28s RNA peaks can be seen at approximately 42 and 48 seconds respectively.

    Journal: BMC Immunology

    Article Title: Successful downstream application of the Paxgene Blood RNA system from small blood samples in paediatric patients for quantitative PCR analysis

    doi: 10.1186/1471-2172-8-20

    Figure Lengend Snippet: Agilent BioAnalyser 2100 traces of total RNA samples. Different volumes of peripheral blood were processed using PAXgene reagent as described in the text. A) Full scale 2.5 mL peripheral blood extraction B) 1.0 mL peripheral blood scaled down extraction C) 0.3 mL peripheral blood scaled down extraction D) Stratagene Universal RNA. The 2.5 mL and 1.0 mL extractions were run on eukaryote total RNA Nano chips and the 0.3 mL extractions and the Universal RNA shown were run on Pico chips. The 18s and 28s RNA peaks can be seen at approximately 42 and 48 seconds respectively.

    Article Snippet: RNA quality was assessed using the Agilent BioAnalyser 2100 and an in-house TaqMan™ assay which measures GAPDH transcript integrity by determining 3' to 5' ratios. qPCR analysis was performed on an additional panel of 7 housekeeping genes.

    Techniques:

    GW-COBRA and LA-COBRA library construction results. ( A ) Sonicated genomic DNA isolated from HCT116 cell line (lane 1), 50 ng of Adapter-2 ligated library material (lane 2). Column purified Adapter-2 ligated library material (lane 3); ( B ) PCR amplification test of bisulfite treated library materials. Lane 1, 2, 3 and 4 are produced by 6, 7, 8 and 9 cycles of PCR using GW-A2-FwdP and COBRA-A2-RevP primers from Table 1 with GW-COBRA library material as the template respectively. Lane 5, 6, 7 and 8 are produced by 6, 7, 8 and 9 cycles of PCR using LA-A2+T7-FwdP and COBRA-A2-RevP primers from Table 1 with LA-COBRA library material as the template, respectively; ( C ) Final library products: GW-COBRA and LA-COBRA methylome libraries of HCT116 DNA amplified using flowcell or LADS primer pairs respectively (Lane 2 and 4). Lane 1 and 3 are negative controls for GW-COBRA and LA-COBRA libraries, respectively; ( D ) Bioanalyzer results of GW-COBRA and LA-COBRA methylome sequencing libraries, respectively, prepared from HCT116 cell line DNA. The final library fragments ranged between 150–500 bp with an average size of 257 and 360 bp for GW-COBRA and LA-COBRA, respectively.

    Journal: Genes

    Article Title: COBRA-Seq: Sensitive and Quantitative Methylome Profiling

    doi: 10.3390/genes6041140

    Figure Lengend Snippet: GW-COBRA and LA-COBRA library construction results. ( A ) Sonicated genomic DNA isolated from HCT116 cell line (lane 1), 50 ng of Adapter-2 ligated library material (lane 2). Column purified Adapter-2 ligated library material (lane 3); ( B ) PCR amplification test of bisulfite treated library materials. Lane 1, 2, 3 and 4 are produced by 6, 7, 8 and 9 cycles of PCR using GW-A2-FwdP and COBRA-A2-RevP primers from Table 1 with GW-COBRA library material as the template respectively. Lane 5, 6, 7 and 8 are produced by 6, 7, 8 and 9 cycles of PCR using LA-A2+T7-FwdP and COBRA-A2-RevP primers from Table 1 with LA-COBRA library material as the template, respectively; ( C ) Final library products: GW-COBRA and LA-COBRA methylome libraries of HCT116 DNA amplified using flowcell or LADS primer pairs respectively (Lane 2 and 4). Lane 1 and 3 are negative controls for GW-COBRA and LA-COBRA libraries, respectively; ( D ) Bioanalyzer results of GW-COBRA and LA-COBRA methylome sequencing libraries, respectively, prepared from HCT116 cell line DNA. The final library fragments ranged between 150–500 bp with an average size of 257 and 360 bp for GW-COBRA and LA-COBRA, respectively.

    Article Snippet: Finally, the size distribution was visualized using Agilent DNA 1000 Assay in 2100 Bioanalyzer (Agilent Technologies, Los Angeles, CA, USA) using the manufacturer’s protocol.

    Techniques: Combined Bisulfite Restriction Analysis Assay, Sonication, Isolation, Purification, Polymerase Chain Reaction, Amplification, Produced, Sequencing

    ( a ) Multiplex ligation-dependent genome amplification (MLGA), reaction scheme.  (I)  Genomic DNA is digested by restriction enzyme to generate targets with defined ends.  (II)  Each MLGA probe consists of two oligonucleotides, one selector oligo of 70–74 nt (green) and one general vector oligo of 34 nt (red). MLGA probe together with DNA-ligase forms circular DNA of target molecules after denaturation and hybridization.  (III)  To reduce background signal in the assay, undesirable, linear DNA is degraded by exonuclease I (Exo I).  (IV)  Multiplex PCR is facilitated by using universal primers that hybridize to a sequence in the vector. PCR products are analyzed using the Agilent Bioanalyzer 2100™ electrophoresis system. ( b ) Data from an MLGA set of 14 probes targeting loci on human chromosomes 13, 18, 21, X and Y. The upper graph shows the resulting elution diagrams from analyses of male and female DNA pools.

    Journal: Nucleic Acids Research

    Article Title: MLGA--a rapid and cost-efficient assay for gene copy-number analysis

    doi: 10.1093/nar/gkm651

    Figure Lengend Snippet: ( a ) Multiplex ligation-dependent genome amplification (MLGA), reaction scheme. (I) Genomic DNA is digested by restriction enzyme to generate targets with defined ends. (II) Each MLGA probe consists of two oligonucleotides, one selector oligo of 70–74 nt (green) and one general vector oligo of 34 nt (red). MLGA probe together with DNA-ligase forms circular DNA of target molecules after denaturation and hybridization. (III) To reduce background signal in the assay, undesirable, linear DNA is degraded by exonuclease I (Exo I). (IV) Multiplex PCR is facilitated by using universal primers that hybridize to a sequence in the vector. PCR products are analyzed using the Agilent Bioanalyzer 2100™ electrophoresis system. ( b ) Data from an MLGA set of 14 probes targeting loci on human chromosomes 13, 18, 21, X and Y. The upper graph shows the resulting elution diagrams from analyses of male and female DNA pools.

    Article Snippet: Temperature cycling was performed as follows: 37° C for 30 min, 95° C for 5 min followed by 30 cycles of 95° C 15 s, 55° C 30 s and 72° C for 60 s followed by 72° C for 10 min. PCR products were analyzed using an Agilent Bioanalyzer 2100™ instrument and quantified using the Agilent 2100 expert software, version B.02.02.SI238.

    Techniques: Multiplex Assay, Ligation, Amplification, Plasmid Preparation, Hybridization, Polymerase Chain Reaction, Sequencing, Electrophoresis

    5-Aza-CdR treatment in vivo leads to inhibition of DNMT1 and apoptosis and results in demethylation of tumor suppressor p16INK4A. A. Cell cycle analysis shows that 5-aza-CdR treatment leads to increased apoptosis. Tumor samples were prepared for FACS analysis as described in the methods section and analyzed with a BD FACSCanto II flow cytometer using the BD FACS Diva Software. Values are means ± SEM. Each value is the mean of three replicates for control and 5-aza-CdR day 5 tumors and of two replicates for 5-aza-CdR day 3 tumors. B. DNMT1 is not detected in tumor protein extracts derived from 5-aza-CdR treated mice. Proteins were extracted from tumor tissue from two tumors treated with 5-aza-CdR starting on day 3 and three tumors treated with 5-aza-CdR on day 5 as described in materials and methods. DNMT1 protein levels were analysed by Western Blot. C. Analysis of the p16 INK4A promotor region by COBRA shows demethylation after 5-aza-CdR treatment. DNA was extracted from tumor tissue, bisulfite converted and analysed by COBRA. Restriction fragments were analysed using the Agilent 2100 Bioanalyzer platform. Normal PBMCs and in vitro by M.SssI methylated PBMCs were used as unmethylated and methylated controls, respectively. Note the re-appearance of the unmethylated fragment in treated samples indicated by the arrow. D. The percentage of methylated fragments is significantly reduced in 5-aza-CdR treated tumors. Percentages of methylated and unmethylated fragments in relation to total peak areas in electropherograms were calculated with Agilent software as described in the methods section.

    Journal: Biochimie

    Article Title: Antineoplastic activity of the DNA methyltransferase inhibitor 5-aza-2?-deoxycytidine in anaplastic large cell lymphoma

    doi: 10.1016/j.biochi.2012.05.029

    Figure Lengend Snippet: 5-Aza-CdR treatment in vivo leads to inhibition of DNMT1 and apoptosis and results in demethylation of tumor suppressor p16INK4A. A. Cell cycle analysis shows that 5-aza-CdR treatment leads to increased apoptosis. Tumor samples were prepared for FACS analysis as described in the methods section and analyzed with a BD FACSCanto II flow cytometer using the BD FACS Diva Software. Values are means ± SEM. Each value is the mean of three replicates for control and 5-aza-CdR day 5 tumors and of two replicates for 5-aza-CdR day 3 tumors. B. DNMT1 is not detected in tumor protein extracts derived from 5-aza-CdR treated mice. Proteins were extracted from tumor tissue from two tumors treated with 5-aza-CdR starting on day 3 and three tumors treated with 5-aza-CdR on day 5 as described in materials and methods. DNMT1 protein levels were analysed by Western Blot. C. Analysis of the p16 INK4A promotor region by COBRA shows demethylation after 5-aza-CdR treatment. DNA was extracted from tumor tissue, bisulfite converted and analysed by COBRA. Restriction fragments were analysed using the Agilent 2100 Bioanalyzer platform. Normal PBMCs and in vitro by M.SssI methylated PBMCs were used as unmethylated and methylated controls, respectively. Note the re-appearance of the unmethylated fragment in treated samples indicated by the arrow. D. The percentage of methylated fragments is significantly reduced in 5-aza-CdR treated tumors. Percentages of methylated and unmethylated fragments in relation to total peak areas in electropherograms were calculated with Agilent software as described in the methods section.

    Article Snippet: Restriction fragments were analyzed on an Agilent 2100 Bioanalyzer platform using the Agilent DNA chip 1000 series.

    Techniques: In Vivo, Inhibition, Cell Cycle Assay, FACS, Flow Cytometry, Cytometry, Software, Derivative Assay, Mouse Assay, Western Blot, Combined Bisulfite Restriction Analysis Assay, In Vitro, Methylation

    5-Aza-CdR treatment leads to demethylation and re-expression of the tumor suppressor p16 INK4A and induces cellular senescence. A. p16 INK4A promoter methylation decreases upon treatment with increasing 5-aza-CdR concentrations. 1 × 10 6 KARPAS-299 cells were incubated with 0, 1 and 10 μM of 5-aza-CdR, the medium was changed after 24 h and then cells were grown for 4 days. DNA was extracted from cells and bisulfite converted and Combined Bisulfite Restriction Analysis (COBRA) was performed to analyse the methylation status of the p16 INK4A promoter as described in materials and methods. Restriction fragments were analysed using the Agilent 2100 Bioanalyzer platform. Note the dose-dependent increase of the unmethylated fragment at 220 bp indicated by the arrow. B. p16 INK4A mRNA increases in the 5-aza-CdR treated cell line KARPAS-299 compared to mock treated controls. RNA was isolated from 1 μM 5-aza-CdR treated KARPAS-299 cells as described in A. p16 INK4A expression was analysed by quantitative RT–PCR. Values are means ± SEM. Each value is the mean of three replicates. Data were analysed by unpaired t -tests. C. Senescent cells accumulate upon 5-aza-CdR treatment. 5-Aza-CdR treated KARPAS-299 and control cells were stained for β-galactosidase activity and counterstained with nuclear fast red. Note the abnormal enlarged shape of 5-aza-CdR treated cells.

    Journal: Biochimie

    Article Title: Antineoplastic activity of the DNA methyltransferase inhibitor 5-aza-2?-deoxycytidine in anaplastic large cell lymphoma

    doi: 10.1016/j.biochi.2012.05.029

    Figure Lengend Snippet: 5-Aza-CdR treatment leads to demethylation and re-expression of the tumor suppressor p16 INK4A and induces cellular senescence. A. p16 INK4A promoter methylation decreases upon treatment with increasing 5-aza-CdR concentrations. 1 × 10 6 KARPAS-299 cells were incubated with 0, 1 and 10 μM of 5-aza-CdR, the medium was changed after 24 h and then cells were grown for 4 days. DNA was extracted from cells and bisulfite converted and Combined Bisulfite Restriction Analysis (COBRA) was performed to analyse the methylation status of the p16 INK4A promoter as described in materials and methods. Restriction fragments were analysed using the Agilent 2100 Bioanalyzer platform. Note the dose-dependent increase of the unmethylated fragment at 220 bp indicated by the arrow. B. p16 INK4A mRNA increases in the 5-aza-CdR treated cell line KARPAS-299 compared to mock treated controls. RNA was isolated from 1 μM 5-aza-CdR treated KARPAS-299 cells as described in A. p16 INK4A expression was analysed by quantitative RT–PCR. Values are means ± SEM. Each value is the mean of three replicates. Data were analysed by unpaired t -tests. C. Senescent cells accumulate upon 5-aza-CdR treatment. 5-Aza-CdR treated KARPAS-299 and control cells were stained for β-galactosidase activity and counterstained with nuclear fast red. Note the abnormal enlarged shape of 5-aza-CdR treated cells.

    Article Snippet: Restriction fragments were analyzed on an Agilent 2100 Bioanalyzer platform using the Agilent DNA chip 1000 series.

    Techniques: Expressing, Methylation, Incubation, Combined Bisulfite Restriction Analysis Assay, Isolation, Quantitative RT-PCR, Staining, Activity Assay

    FFAR2 has numerous copies in European broiler and in ancestral chicken genome. qPCR on genomic DNA shows clear difference in ΔCq between FFAR2 genes and the genes carrying only one copy per genome (four genes in European lines and three genes in Ancestral lines). qPCR was performed using “universal” primers able to amplify the 26 sequences of FFAR2 (see supplementary data S1 , Supplementary Material online). FFAR2 error bars indicate standard deviation between two individual chickens. For the single copy genes, error bars represent standard deviation between the Cq measures for the three or four genes from two individual chickens.

    Journal: Genome Biology and Evolution

    Article Title: Expanding Duplication of Free Fatty Acid Receptor-2 (GPR43) Genes in the Chicken Genome

    doi: 10.1093/gbe/evv072

    Figure Lengend Snippet: FFAR2 has numerous copies in European broiler and in ancestral chicken genome. qPCR on genomic DNA shows clear difference in ΔCq between FFAR2 genes and the genes carrying only one copy per genome (four genes in European lines and three genes in Ancestral lines). qPCR was performed using “universal” primers able to amplify the 26 sequences of FFAR2 (see supplementary data S1 , Supplementary Material online). FFAR2 error bars indicate standard deviation between two individual chickens. For the single copy genes, error bars represent standard deviation between the Cq measures for the three or four genes from two individual chickens.

    Article Snippet: Libraries were then checked on an Agilent Technologies 2100 Bioanalyzer using the Agilent High Sensitivity DNA Kit and quantified by qPCR with the QPCR NGS Library Quantification kit (Agilent Technologies).

    Techniques: Real-time Polymerase Chain Reaction, Standard Deviation

    Characterization of exosomal RNA (esRNA) extracted from purified nanovesicles from fresh human aqueous humor. The esRNA was evaluated using Agilent Bioanalyzer 2100 with Agilent RNA 6000 Pico Kit. A) Shows the RNA ladder and B) displays extracted esRNA from one of the human aqueous humor samples. The size of extracted esRNA was less than 200 nucleotides (nt), mostly around 25 nt. C) shows the miRNAs that were identified via small RNA sequencing using Illumina MiSeq sequencing system. The height of each bar indicated the number of sequence reads with perfect match to mature miRNA.

    Journal: Experimental eye research

    Article Title: Human Aqueous Humor Exosomes

    doi: 10.1016/j.exer.2015.01.019

    Figure Lengend Snippet: Characterization of exosomal RNA (esRNA) extracted from purified nanovesicles from fresh human aqueous humor. The esRNA was evaluated using Agilent Bioanalyzer 2100 with Agilent RNA 6000 Pico Kit. A) Shows the RNA ladder and B) displays extracted esRNA from one of the human aqueous humor samples. The size of extracted esRNA was less than 200 nucleotides (nt), mostly around 25 nt. C) shows the miRNAs that were identified via small RNA sequencing using Illumina MiSeq sequencing system. The height of each bar indicated the number of sequence reads with perfect match to mature miRNA.

    Article Snippet: Quality of extracted esRNA was evaluated using Agilent Bioanalyzer 2100 with Agilent RNA 6000 Pico Kit.

    Techniques: Purification, RNA Sequencing Assay, Sequencing