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  • 93
    Agilent technologies 2100 bioanalyzer bioa
    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 <t>2100</t> <t>Bioanalyzer</t> 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.
    2100 Bioanalyzer Bioa, supplied by Agilent technologies, used in various techniques. Bioz Stars score: 93/100, based on 4279 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/2100 bioanalyzer bioa/product/Agilent technologies
    Average 93 stars, based on 4279 article reviews
    Price from $9.99 to $1999.99
    2100 bioanalyzer bioa - by Bioz Stars, 2020-05
    93/100 stars
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    92
    Thermo Fisher bioanalyzer 2100
    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 <t>2100</t> <t>Bioanalyzer</t> 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.
    Bioanalyzer 2100, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 92/100, based on 439 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioanalyzer 2100/product/Thermo Fisher
    Average 92 stars, based on 439 article reviews
    Price from $9.99 to $1999.99
    bioanalyzer 2100 - by Bioz Stars, 2020-05
    92/100 stars
      Buy from Supplier

    92
    Stratagene bioanalyzer 2100
    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 <t>2100</t> <t>Bioanalyzer</t> 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.
    Bioanalyzer 2100, supplied by Stratagene, used in various techniques. Bioz Stars score: 92/100, based on 68 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/bioanalyzer 2100/product/Stratagene
    Average 92 stars, based on 68 article reviews
    Price from $9.99 to $1999.99
    bioanalyzer 2100 - by Bioz Stars, 2020-05
    92/100 stars
      Buy from Supplier

    92
    Hewlett-Packard agilent bioanalyzer 2100
    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 <t>2100</t> <t>Bioanalyzer</t> 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.
    Agilent Bioanalyzer 2100, supplied by Hewlett-Packard, used in various techniques. Bioz Stars score: 92/100, based on 37 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/agilent bioanalyzer 2100/product/Hewlett-Packard
    Average 92 stars, based on 37 article reviews
    Price from $9.99 to $1999.99
    agilent bioanalyzer 2100 - by Bioz Stars, 2020-05
    92/100 stars
      Buy from Supplier

    91
    Santa Cruz Biotechnology agilent bioanalyzer 2100
    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 <t>2100</t> <t>Bioanalyzer</t> 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.
    Agilent Bioanalyzer 2100, supplied by Santa Cruz Biotechnology, used in various techniques. Bioz Stars score: 91/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/agilent bioanalyzer 2100/product/Santa Cruz Biotechnology
    Average 91 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    agilent bioanalyzer 2100 - by Bioz Stars, 2020-05
    91/100 stars
      Buy from Supplier

    Image Search Results


    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

    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

    Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent 2100 Bioanalyzer. The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.

    Journal: Oncotarget

    Article Title: Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations

    doi: 10.18632/oncotarget.11796

    Figure Lengend Snippet: Mutation g.chrX:70339329T > C in MED12 causes the splicing of exon 2 ( A ) Schematic representation of the normal (top) and aberrant splicing (bottom) of MED12 transcripts from the normal and the identified mutant gene. In the presence of the mutation, the donor splice site of exon 2 (underlined) is skipped and exon 1 is directly spliced to exon 3, leading to an aberrant mature form of MED12 mRNA lacking exon 2. ( B ) Synthetic electrophoresis gel of MED12 PCR products (Methods). cDNAs were synthesized from mature RNA extracted from patient 744 mutated at g.chrX :70339329T > C, REH cells, mature T-cells (CD19-CD3+) isolated from cord blood samples and two T-ALL patients, WT for this position (791 and 727). Amplified fragments of 281 bp (WT samples) and 176 bp (mutated sample) were analyzed using Agilent 2100 Bioanalyzer. The 105 bp difference corresponds to the skipped exon 2. L: ladder; CTL-: negative control. ( C ) Screenshot of the Integrative Genomics Viewer (IGV) window presenting aligned RNA-seq data obtained from cases 744 (top) and a third T-ALL WT patient (693, bottom). The dotted line is centered on the donor splice site of exon 2 of MED12 (g.chrX:70339329). Case 744 shows aberrant splicing of exon 2, while 693 was WT for this position and shows a mature transcript that includes the exon 2.

    Article Snippet: Amplified fragments were analyzed on the Agilent 2100 Bioanalyzer Instrument and by Sanger sequencing (McGill University and Genome Quebec Innovation Centre).

    Techniques: Mutagenesis, Electrophoresis, Polymerase Chain Reaction, Synthesized, Isolation, Amplification, CTL Assay, Negative Control, RNA Sequencing Assay

    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

    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

    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

    ( 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