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    AceSeq Saliva DNA Isolation Kit provides a fast and simple spin column procedure for isolating high quality DNA from saliva samples collected and preserved using AcceGen s Saliva DNA Collection
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    Thermo Fisher gdna
    ChIP-STARR-Seq in Human Embryonic Stem Cells (A) Outline of the ChIP-STARR-seq approach combining antibodies against TFs or histone modifications (colored balls) with the STARR-seq plasmid ( Arnold et al., 2013 ). (B) ChIP-STARR-seq for NANOG in H9. Scatterplots compare normalized read count (reads per million) per peak between datasets, obtained from ChIP-seq or <t>DNA-seq</t> of plasmid libraries pre- or post-transfection/recovery from ESCs (n = 2); r , Pearson correlation. (C) Genomic distribution of peaks called for ChIP-seq (outer chart) and corresponding plasmid libraries (inner chart). TSSs, transcription start sites. (D) FACS plots of single DAPI-negative ESCs. Left: untransfected cells; right: cells transfected with a NANOG ChIP-STARR-seq plasmid library. (E) Scatterplot (like in B) comparing the NANOG plasmid library and corresponding ChIP-STARR-seq <t>RNA.</t> The dense cluster of points in the lower left corresponds to library plasmids that did not produce RNAs. RPM, reads per million. (F) Genome browser plot of SOX2 showing tracks for ChIP-seq, DNA-seq of plasmid libraries pre- and post-transfection, and from RNA-seq of GFP + cells transfected with the indicated libraries. Bottom: combination (maximum) of all STARR-seq RNA-seq tracks and ratio of normalized RNA-seq/plasmid reads. (G) Genome browser shots of KLF15, LEFTY , and HOXB cluster, illustrating a broad variety of enhancers profiled in this functional enhancer catalog.
    Gdna, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 10432 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Gentra Systems puregene dna isolation kit
    Inhibition of Dam activity by compound 14 in (A) Y. pseudotuberculosis and (B) Y. pestis . Genomic <t>DNA</t> (2 μg) was isolated using the <t>Puregene</t> DNA isolation kit (Gentra Systems, Minneapolis, USA) from (A) Y. pseudotuberculosis and (B) Y. pestis
    Puregene Dna Isolation Kit, supplied by Gentra Systems, used in various techniques. Bioz Stars score: 94/100, based on 4481 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen powerwater dna isolation kit
    Inhibition of Dam activity by compound 14 in (A) Y. pseudotuberculosis and (B) Y. pestis . Genomic <t>DNA</t> (2 μg) was isolated using the <t>Puregene</t> DNA isolation kit (Gentra Systems, Minneapolis, USA) from (A) Y. pseudotuberculosis and (B) Y. pestis
    Powerwater Dna Isolation Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 1356 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Meridian Life Science isolate ii genomic dna kit
    Application of TIDER to in vivo edited <t>DNA</t> sequences. Comparison of TIDER and NGS analyses of various mutations introduced by template-directed Cas9 editing in human cell line <t>RPE</t> ( A–D, F ) and mouse ES cells ( E ). In each panel (a-e), a pool of cells was treated with Cas9, a targeting sgRNA and a ssODN carrying 3–4 mutations. Panel ( F ) shows a control experiment corresponding to ( D ) in which the ssODN was omitted. Additional control experiments corresponding to ( A–C . In each panel, the top sequence corresponds to wild-type, with the sgRNA sequence highlighted in grey and the expected cut site marked by a vertical line; the bottom sequence indicates the designed mutant, with mutated nucleotides highlighted in green. Bar graphs show the estimated percentage of successfully edited DNA molecules (right-hand plot; ‘HDR’) and of indels of the indicated size (left-hand plot). Upward axes show TIDER estimates; downward axes show the NGS estimates based on the same DNA sample. Pale red and blue bars indicate proportions of wild-type (non-mutated) sequence. R 2 values indicate the goodness-of-fit score for the TIDER estimates; ‘total eff’ indicates the total according to TIDER (top) and NGS (bottom); ‘other mutations’ are all non-indel, non-designed mutations as detected by NGS (and which cannot be detected by TIDER). For TIDER, the decomposition was limited to deletions of sizes 0–15 and insertions of sizes 0–5. For NGS, at least 2 × 10 4 reads were analyzed in each experiment.
    Isolate Ii Genomic Dna Kit, supplied by Meridian Life Science, used in various techniques. Bioz Stars score: 91/100, based on 532 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen dna isolation kit
    Application of TIDER to in vivo edited <t>DNA</t> sequences. Comparison of TIDER and NGS analyses of various mutations introduced by template-directed Cas9 editing in human cell line <t>RPE</t> ( A–D, F ) and mouse ES cells ( E ). In each panel (a-e), a pool of cells was treated with Cas9, a targeting sgRNA and a ssODN carrying 3–4 mutations. Panel ( F ) shows a control experiment corresponding to ( D ) in which the ssODN was omitted. Additional control experiments corresponding to ( A–C . In each panel, the top sequence corresponds to wild-type, with the sgRNA sequence highlighted in grey and the expected cut site marked by a vertical line; the bottom sequence indicates the designed mutant, with mutated nucleotides highlighted in green. Bar graphs show the estimated percentage of successfully edited DNA molecules (right-hand plot; ‘HDR’) and of indels of the indicated size (left-hand plot). Upward axes show TIDER estimates; downward axes show the NGS estimates based on the same DNA sample. Pale red and blue bars indicate proportions of wild-type (non-mutated) sequence. R 2 values indicate the goodness-of-fit score for the TIDER estimates; ‘total eff’ indicates the total according to TIDER (top) and NGS (bottom); ‘other mutations’ are all non-indel, non-designed mutations as detected by NGS (and which cannot be detected by TIDER). For TIDER, the decomposition was limited to deletions of sizes 0–15 and insertions of sizes 0–5. For NGS, at least 2 × 10 4 reads were analyzed in each experiment.
    Dna Isolation Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 2630 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen powersoil dna isolation kit
    Application of TIDER to in vivo edited <t>DNA</t> sequences. Comparison of TIDER and NGS analyses of various mutations introduced by template-directed Cas9 editing in human cell line <t>RPE</t> ( A–D, F ) and mouse ES cells ( E ). In each panel (a-e), a pool of cells was treated with Cas9, a targeting sgRNA and a ssODN carrying 3–4 mutations. Panel ( F ) shows a control experiment corresponding to ( D ) in which the ssODN was omitted. Additional control experiments corresponding to ( A–C . In each panel, the top sequence corresponds to wild-type, with the sgRNA sequence highlighted in grey and the expected cut site marked by a vertical line; the bottom sequence indicates the designed mutant, with mutated nucleotides highlighted in green. Bar graphs show the estimated percentage of successfully edited DNA molecules (right-hand plot; ‘HDR’) and of indels of the indicated size (left-hand plot). Upward axes show TIDER estimates; downward axes show the NGS estimates based on the same DNA sample. Pale red and blue bars indicate proportions of wild-type (non-mutated) sequence. R 2 values indicate the goodness-of-fit score for the TIDER estimates; ‘total eff’ indicates the total according to TIDER (top) and NGS (bottom); ‘other mutations’ are all non-indel, non-designed mutations as detected by NGS (and which cannot be detected by TIDER). For TIDER, the decomposition was limited to deletions of sizes 0–15 and insertions of sizes 0–5. For NGS, at least 2 × 10 4 reads were analyzed in each experiment.
    Powersoil Dna Isolation Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 13284 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Gentra Systems dna isolation kit
    The Foxl2 promoter is hypomethylated in homologous cells and tissues. A) Analysis of percent methylation of two regions of the Foxl2 promoter in genomic <t>DNA</t> from <t>LβT2</t> and NIH3T3 cells as assessed by qAMP (white bars) and pyrosequencing (black bars). Data are from a representative of a 2 replicate experiments, which yielded comparable results. B) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine cell lines. Data are from a single experiment. C) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine tissues Data are from a representative of a 2 replicate experiments, which yielded comparable results.
    Dna Isolation Kit, supplied by Gentra Systems, used in various techniques. Bioz Stars score: 93/100, based on 562 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher magmax cfdna isolation kit
    The Foxl2 promoter is hypomethylated in homologous cells and tissues. A) Analysis of percent methylation of two regions of the Foxl2 promoter in genomic <t>DNA</t> from <t>LβT2</t> and NIH3T3 cells as assessed by qAMP (white bars) and pyrosequencing (black bars). Data are from a representative of a 2 replicate experiments, which yielded comparable results. B) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine cell lines. Data are from a single experiment. C) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine tissues Data are from a representative of a 2 replicate experiments, which yielded comparable results.
    Magmax Cfdna Isolation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 30 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Millipore dna isolation
    The Foxl2 promoter is hypomethylated in homologous cells and tissues. A) Analysis of percent methylation of two regions of the Foxl2 promoter in genomic <t>DNA</t> from <t>LβT2</t> and NIH3T3 cells as assessed by qAMP (white bars) and pyrosequencing (black bars). Data are from a representative of a 2 replicate experiments, which yielded comparable results. B) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine cell lines. Data are from a single experiment. C) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine tissues Data are from a representative of a 2 replicate experiments, which yielded comparable results.
    Dna Isolation, supplied by Millipore, used in various techniques. Bioz Stars score: 99/100, based on 194 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega wizard genomic dna isolation kit
    The Foxl2 promoter is hypomethylated in homologous cells and tissues. A) Analysis of percent methylation of two regions of the Foxl2 promoter in genomic <t>DNA</t> from <t>LβT2</t> and NIH3T3 cells as assessed by qAMP (white bars) and pyrosequencing (black bars). Data are from a representative of a 2 replicate experiments, which yielded comparable results. B) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine cell lines. Data are from a single experiment. C) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine tissues Data are from a representative of a 2 replicate experiments, which yielded comparable results.
    Wizard Genomic Dna Isolation Kit, supplied by Promega, used in various techniques. Bioz Stars score: 90/100, based on 634 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tiangen biotech co dna isolation kit
    miR-29c-3p directly targets <t>DNA</t> methyltransferase 3B (DNMT3B) and miR-29c-3p levels were inversely correlated with DNMT3B protein levels. a Venn diagram displaying miR-29c-3p computationally predicted to target DNMT3B by four different prediction algorithms: TargetScan, MiRanda, Oncomir, and miRWalk. b miR-29c-3p expression was negatively correlated with DNMT3B expression in hepatocellular carcinoma (HCC) tissues. Spearman's rank test ( r = −0.751, p
    Dna Isolation Kit, supplied by tiangen biotech co, used in various techniques. Bioz Stars score: 93/100, based on 437 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Promega dna isolation kit
    miR-29c-3p directly targets <t>DNA</t> methyltransferase 3B (DNMT3B) and miR-29c-3p levels were inversely correlated with DNMT3B protein levels. a Venn diagram displaying miR-29c-3p computationally predicted to target DNMT3B by four different prediction algorithms: TargetScan, MiRanda, Oncomir, and miRWalk. b miR-29c-3p expression was negatively correlated with DNMT3B expression in hepatocellular carcinoma (HCC) tissues. Spearman's rank test ( r = −0.751, p
    Dna Isolation Kit, supplied by Promega, used in various techniques. Bioz Stars score: 93/100, based on 471 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Norgen Biotek phage dna isolation kit
    miR-29c-3p directly targets <t>DNA</t> methyltransferase 3B (DNMT3B) and miR-29c-3p levels were inversely correlated with DNMT3B protein levels. a Venn diagram displaying miR-29c-3p computationally predicted to target DNMT3B by four different prediction algorithms: TargetScan, MiRanda, Oncomir, and miRWalk. b miR-29c-3p expression was negatively correlated with DNMT3B expression in hepatocellular carcinoma (HCC) tissues. Spearman's rank test ( r = −0.751, p
    Phage Dna Isolation Kit, supplied by Norgen Biotek, used in various techniques. Bioz Stars score: 99/100, based on 404 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen biostic bacteremia dna isolation kit
    miR-29c-3p directly targets <t>DNA</t> methyltransferase 3B (DNMT3B) and miR-29c-3p levels were inversely correlated with DNMT3B protein levels. a Venn diagram displaying miR-29c-3p computationally predicted to target DNMT3B by four different prediction algorithms: TargetScan, MiRanda, Oncomir, and miRWalk. b miR-29c-3p expression was negatively correlated with DNMT3B expression in hepatocellular carcinoma (HCC) tissues. Spearman's rank test ( r = −0.751, p
    Biostic Bacteremia Dna Isolation Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 212 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Bio-Rad aquapure genomic dna isolation kit
    miR-29c-3p directly targets <t>DNA</t> methyltransferase 3B (DNMT3B) and miR-29c-3p levels were inversely correlated with DNMT3B protein levels. a Venn diagram displaying miR-29c-3p computationally predicted to target DNMT3B by four different prediction algorithms: TargetScan, MiRanda, Oncomir, and miRWalk. b miR-29c-3p expression was negatively correlated with DNMT3B expression in hepatocellular carcinoma (HCC) tissues. Spearman's rank test ( r = −0.751, p
    Aquapure Genomic Dna Isolation Kit, supplied by Bio-Rad, used in various techniques. Bioz Stars score: 89/100, based on 395 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    MACHEREY NAGEL dna isolation
    miR-29c-3p directly targets <t>DNA</t> methyltransferase 3B (DNMT3B) and miR-29c-3p levels were inversely correlated with DNMT3B protein levels. a Venn diagram displaying miR-29c-3p computationally predicted to target DNMT3B by four different prediction algorithms: TargetScan, MiRanda, Oncomir, and miRWalk. b miR-29c-3p expression was negatively correlated with DNMT3B expression in hepatocellular carcinoma (HCC) tissues. Spearman's rank test ( r = −0.751, p
    Dna Isolation, supplied by MACHEREY NAGEL, used in various techniques. Bioz Stars score: 94/100, based on 116 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Thermo Fisher dna isolation kit
    ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the <t>DNA</t> bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, <t>GeneRuler</t> 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence
    Dna Isolation Kit, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 381 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen qiaamp dna isolation kit
    ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the <t>DNA</t> bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, <t>GeneRuler</t> 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence
    Qiaamp Dna Isolation Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 322 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Illumina Inc dna isolation
    ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the <t>DNA</t> bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, <t>GeneRuler</t> 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence
    Dna Isolation, supplied by Illumina Inc, used in various techniques. Bioz Stars score: 94/100, based on 148 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    tiangen biotech co dna isolation
    ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the <t>DNA</t> bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, <t>GeneRuler</t> 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence
    Dna Isolation, supplied by tiangen biotech co, used in various techniques. Bioz Stars score: 94/100, based on 121 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Qiagen puregene dna isolation kit
    ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the <t>DNA</t> bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, <t>GeneRuler</t> 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence
    Puregene Dna Isolation Kit, supplied by Qiagen, used in various techniques. Bioz Stars score: 99/100, based on 838 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Gentra Systems dna isolation
    ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the <t>DNA</t> bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, <t>GeneRuler</t> 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence
    Dna Isolation, supplied by Gentra Systems, used in various techniques. Bioz Stars score: 92/100, based on 87 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Isolation of high quality DNA from blood in sufficient quantities is crucial for clinical research and forensic analysis BioVision s Whole Blood DNA Isolation Kit facilitates purification of quality DNA
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    TIAN amp DNA RNA Isolation Kits are designed for extracting both genomic DNA and total RNA simultaneous from the same animal cells or tissue sample This kit is compatible with
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    ChIP-STARR-Seq in Human Embryonic Stem Cells (A) Outline of the ChIP-STARR-seq approach combining antibodies against TFs or histone modifications (colored balls) with the STARR-seq plasmid ( Arnold et al., 2013 ). (B) ChIP-STARR-seq for NANOG in H9. Scatterplots compare normalized read count (reads per million) per peak between datasets, obtained from ChIP-seq or DNA-seq of plasmid libraries pre- or post-transfection/recovery from ESCs (n = 2); r , Pearson correlation. (C) Genomic distribution of peaks called for ChIP-seq (outer chart) and corresponding plasmid libraries (inner chart). TSSs, transcription start sites. (D) FACS plots of single DAPI-negative ESCs. Left: untransfected cells; right: cells transfected with a NANOG ChIP-STARR-seq plasmid library. (E) Scatterplot (like in B) comparing the NANOG plasmid library and corresponding ChIP-STARR-seq RNA. The dense cluster of points in the lower left corresponds to library plasmids that did not produce RNAs. RPM, reads per million. (F) Genome browser plot of SOX2 showing tracks for ChIP-seq, DNA-seq of plasmid libraries pre- and post-transfection, and from RNA-seq of GFP + cells transfected with the indicated libraries. Bottom: combination (maximum) of all STARR-seq RNA-seq tracks and ratio of normalized RNA-seq/plasmid reads. (G) Genome browser shots of KLF15, LEFTY , and HOXB cluster, illustrating a broad variety of enhancers profiled in this functional enhancer catalog.

    Journal: Cell Stem Cell

    Article Title: Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells

    doi: 10.1016/j.stem.2018.06.014

    Figure Lengend Snippet: ChIP-STARR-Seq in Human Embryonic Stem Cells (A) Outline of the ChIP-STARR-seq approach combining antibodies against TFs or histone modifications (colored balls) with the STARR-seq plasmid ( Arnold et al., 2013 ). (B) ChIP-STARR-seq for NANOG in H9. Scatterplots compare normalized read count (reads per million) per peak between datasets, obtained from ChIP-seq or DNA-seq of plasmid libraries pre- or post-transfection/recovery from ESCs (n = 2); r , Pearson correlation. (C) Genomic distribution of peaks called for ChIP-seq (outer chart) and corresponding plasmid libraries (inner chart). TSSs, transcription start sites. (D) FACS plots of single DAPI-negative ESCs. Left: untransfected cells; right: cells transfected with a NANOG ChIP-STARR-seq plasmid library. (E) Scatterplot (like in B) comparing the NANOG plasmid library and corresponding ChIP-STARR-seq RNA. The dense cluster of points in the lower left corresponds to library plasmids that did not produce RNAs. RPM, reads per million. (F) Genome browser plot of SOX2 showing tracks for ChIP-seq, DNA-seq of plasmid libraries pre- and post-transfection, and from RNA-seq of GFP + cells transfected with the indicated libraries. Bottom: combination (maximum) of all STARR-seq RNA-seq tracks and ratio of normalized RNA-seq/plasmid reads. (G) Genome browser shots of KLF15, LEFTY , and HOXB cluster, illustrating a broad variety of enhancers profiled in this functional enhancer catalog.

    Article Snippet: 1 μg of RNA was treated with DNaseI (Invitrogen) to remove genomic DNA contamination and cDNA was obtained through reverse transcription using SuperScriptIII (Invitrogen) in the presence of RNaseOUT (Invitrogen). cDNA was diluted in DEPC-treated water to a final volume of 200 μL and 2 μL of cDNA was used per qPCR reaction, using a 2x Takyon qPCR master mix (No ROX SYBR, UF-NSMT-B0701, Takyon). qPCR reactions were run on a Roche Lightcycler 480 II (Roche), using the following cycle conditions: 95°C 3 min, (95°C 10 s, 60°C 30 s, 72°C 25 s) x45, followed by a melting curve from 95° to 65°C.

    Techniques: Chromatin Immunoprecipitation, Plasmid Preparation, DNA Sequencing, Transfection, FACS, RNA Sequencing Assay, Functional Assay

    Inhibition of Dam activity by compound 14 in (A) Y. pseudotuberculosis and (B) Y. pestis . Genomic DNA (2 μg) was isolated using the Puregene DNA isolation kit (Gentra Systems, Minneapolis, USA) from (A) Y. pseudotuberculosis and (B) Y. pestis

    Journal: British Journal of Pharmacology

    Article Title: Inhibition of Yersinia pestis DNA adenine methyltransferase in vitro by a stibonic acid compound: identification of a potential novel class of antimicrobial agents

    doi: 10.1111/j.1476-5381.2012.02134.x

    Figure Lengend Snippet: Inhibition of Dam activity by compound 14 in (A) Y. pseudotuberculosis and (B) Y. pestis . Genomic DNA (2 μg) was isolated using the Puregene DNA isolation kit (Gentra Systems, Minneapolis, USA) from (A) Y. pseudotuberculosis and (B) Y. pestis

    Article Snippet: Genomic DNA (2 μg) was isolated using the Puregene DNA isolation kit (Gentra Systems, Minneapolis, MN, USA) and digested by one of the restriction endonucleases, Mbo I, Sau 3AI or Dpn I (Promega, Southampton, UK) for 4 h at 37°C.

    Techniques: Inhibition, Activity Assay, Isolation, DNA Extraction

    Application of TIDER to in vivo edited DNA sequences. Comparison of TIDER and NGS analyses of various mutations introduced by template-directed Cas9 editing in human cell line RPE ( A–D, F ) and mouse ES cells ( E ). In each panel (a-e), a pool of cells was treated with Cas9, a targeting sgRNA and a ssODN carrying 3–4 mutations. Panel ( F ) shows a control experiment corresponding to ( D ) in which the ssODN was omitted. Additional control experiments corresponding to ( A–C . In each panel, the top sequence corresponds to wild-type, with the sgRNA sequence highlighted in grey and the expected cut site marked by a vertical line; the bottom sequence indicates the designed mutant, with mutated nucleotides highlighted in green. Bar graphs show the estimated percentage of successfully edited DNA molecules (right-hand plot; ‘HDR’) and of indels of the indicated size (left-hand plot). Upward axes show TIDER estimates; downward axes show the NGS estimates based on the same DNA sample. Pale red and blue bars indicate proportions of wild-type (non-mutated) sequence. R 2 values indicate the goodness-of-fit score for the TIDER estimates; ‘total eff’ indicates the total according to TIDER (top) and NGS (bottom); ‘other mutations’ are all non-indel, non-designed mutations as detected by NGS (and which cannot be detected by TIDER). For TIDER, the decomposition was limited to deletions of sizes 0–15 and insertions of sizes 0–5. For NGS, at least 2 × 10 4 reads were analyzed in each experiment.

    Journal: Nucleic Acids Research

    Article Title: Easy quantification of template-directed CRISPR/Cas9 editing

    doi: 10.1093/nar/gky164

    Figure Lengend Snippet: Application of TIDER to in vivo edited DNA sequences. Comparison of TIDER and NGS analyses of various mutations introduced by template-directed Cas9 editing in human cell line RPE ( A–D, F ) and mouse ES cells ( E ). In each panel (a-e), a pool of cells was treated with Cas9, a targeting sgRNA and a ssODN carrying 3–4 mutations. Panel ( F ) shows a control experiment corresponding to ( D ) in which the ssODN was omitted. Additional control experiments corresponding to ( A–C . In each panel, the top sequence corresponds to wild-type, with the sgRNA sequence highlighted in grey and the expected cut site marked by a vertical line; the bottom sequence indicates the designed mutant, with mutated nucleotides highlighted in green. Bar graphs show the estimated percentage of successfully edited DNA molecules (right-hand plot; ‘HDR’) and of indels of the indicated size (left-hand plot). Upward axes show TIDER estimates; downward axes show the NGS estimates based on the same DNA sample. Pale red and blue bars indicate proportions of wild-type (non-mutated) sequence. R 2 values indicate the goodness-of-fit score for the TIDER estimates; ‘total eff’ indicates the total according to TIDER (top) and NGS (bottom); ‘other mutations’ are all non-indel, non-designed mutations as detected by NGS (and which cannot be detected by TIDER). For TIDER, the decomposition was limited to deletions of sizes 0–15 and insertions of sizes 0–5. For NGS, at least 2 × 10 4 reads were analyzed in each experiment.

    Article Snippet: Genomic DNA was isolated 2 days (RPE cells) or 7 days (mESC cells) after transfection using either the Isolate II Genomic DNA Kit (Bioline) or lysisbuffer (100 mM Tris (pH 8.5), 50 mM EDTA, 40 mM NaCl, 0.2% SDS and 100 ug/ml proteinase K) for 2 h at 55°C.

    Techniques: In Vivo, Next-Generation Sequencing, Sequencing, Mutagenesis

    The Foxl2 promoter is hypomethylated in homologous cells and tissues. A) Analysis of percent methylation of two regions of the Foxl2 promoter in genomic DNA from LβT2 and NIH3T3 cells as assessed by qAMP (white bars) and pyrosequencing (black bars). Data are from a representative of a 2 replicate experiments, which yielded comparable results. B) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine cell lines. Data are from a single experiment. C) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine tissues Data are from a representative of a 2 replicate experiments, which yielded comparable results.

    Journal: PLoS ONE

    Article Title: The CpG Island in the Murine Foxl2 Proximal Promoter Is Differentially Methylated in Primary and Immortalized Cells

    doi: 10.1371/journal.pone.0076642

    Figure Lengend Snippet: The Foxl2 promoter is hypomethylated in homologous cells and tissues. A) Analysis of percent methylation of two regions of the Foxl2 promoter in genomic DNA from LβT2 and NIH3T3 cells as assessed by qAMP (white bars) and pyrosequencing (black bars). Data are from a representative of a 2 replicate experiments, which yielded comparable results. B) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine cell lines. Data are from a single experiment. C) Percent methylation of -81/+43 of the Foxl2 promoter in genomic DNA from the indicated murine tissues Data are from a representative of a 2 replicate experiments, which yielded comparable results.

    Article Snippet: CpG methylation analysis by pyrosequencing Genomic DNA from LβT2, TαT-1, and NIH3T3 cells was extracted using the Gentra Systems DNA Isolation kit and samples sent to EpigenDx (Hopkinton, MA) for CpG methylation analysis.

    Techniques: Methylation

    The murine Foxl2 promoter is differentially methylated in homologous and heterologous cells. A) DNA sequence (-600 to +165) of the murine Foxl2 promoter. Of 62 CpG dinucleotides pictured, 51 were analyzed by pyrosequencing (shaded in grey). The transcriptional start site (+1) mapped here by 5’ RACE is indicated with an arrow. The ATG translation initiation codon is underlined. The first nucleotides of the -432 and -187 reporters are marked above the sequence with * and **, respectively. B) Percent methylation of the CpGs at the indicated positions in genomic DNA from LβT2 (white bars), TαT1 (grey bars), and NIH3T3 (black bars) cell lines as assessed by pyrosequencing.

    Journal: PLoS ONE

    Article Title: The CpG Island in the Murine Foxl2 Proximal Promoter Is Differentially Methylated in Primary and Immortalized Cells

    doi: 10.1371/journal.pone.0076642

    Figure Lengend Snippet: The murine Foxl2 promoter is differentially methylated in homologous and heterologous cells. A) DNA sequence (-600 to +165) of the murine Foxl2 promoter. Of 62 CpG dinucleotides pictured, 51 were analyzed by pyrosequencing (shaded in grey). The transcriptional start site (+1) mapped here by 5’ RACE is indicated with an arrow. The ATG translation initiation codon is underlined. The first nucleotides of the -432 and -187 reporters are marked above the sequence with * and **, respectively. B) Percent methylation of the CpGs at the indicated positions in genomic DNA from LβT2 (white bars), TαT1 (grey bars), and NIH3T3 (black bars) cell lines as assessed by pyrosequencing.

    Article Snippet: CpG methylation analysis by pyrosequencing Genomic DNA from LβT2, TαT-1, and NIH3T3 cells was extracted using the Gentra Systems DNA Isolation kit and samples sent to EpigenDx (Hopkinton, MA) for CpG methylation analysis.

    Techniques: Methylation, Sequencing

    miR-29c-3p directly targets DNA methyltransferase 3B (DNMT3B) and miR-29c-3p levels were inversely correlated with DNMT3B protein levels. a Venn diagram displaying miR-29c-3p computationally predicted to target DNMT3B by four different prediction algorithms: TargetScan, MiRanda, Oncomir, and miRWalk. b miR-29c-3p expression was negatively correlated with DNMT3B expression in hepatocellular carcinoma (HCC) tissues. Spearman's rank test ( r = −0.751, p

    Journal: Cell Death & Disease

    Article Title: miR-29c-3p regulates DNMT3B and LATS1 methylation to inhibit tumor progression in hepatocellular carcinoma

    doi: 10.1038/s41419-018-1281-7

    Figure Lengend Snippet: miR-29c-3p directly targets DNA methyltransferase 3B (DNMT3B) and miR-29c-3p levels were inversely correlated with DNMT3B protein levels. a Venn diagram displaying miR-29c-3p computationally predicted to target DNMT3B by four different prediction algorithms: TargetScan, MiRanda, Oncomir, and miRWalk. b miR-29c-3p expression was negatively correlated with DNMT3B expression in hepatocellular carcinoma (HCC) tissues. Spearman's rank test ( r = −0.751, p

    Article Snippet: Genomic DNA was isolated from HCC tumor tissues, paired normal adjacent tissues, and HCC cells using the DNA Isolation kit (Tiangen, Beijing, China) according to the manufacturer’s protocol.

    Techniques: Expressing

    DNA methyltransferase 3B (DNMT3B) is upregulated and large tumor suppressor gene 1 (LATS1) is downregulated in hepatocellular carcinoma (HCC). a Quantitative real-time PCR (qRT-PCR) analysis of DNMT3B expression in 150 pairs of HCC tissues and paired normal adjacent tissues. b qRT-PCR analysis of LATS1 expression in 150 pairs of HCC tissues and paired normal adjacent tissues. c Immunohistochemical staining analysis of DNMT3B protein expression levels in HCC tissues. d Immunohistochemical staining analysis of LATS1 protein expression levels in HCC tissues. e Kaplan–Meier analysis of overall survival between HCC patients with high and low DNMT3B expression. f Kaplan–Meier analysis of overall survival between high and low LATS1 expression in HCC patients. g Kaplan–Meier analysis of overall survival between the high miR-29c-3p/low DNMT3B/high LATS1 expression group and low miR-29c-3p/high DNMT3B/low LATS1 expression group; ** p

    Journal: Cell Death & Disease

    Article Title: miR-29c-3p regulates DNMT3B and LATS1 methylation to inhibit tumor progression in hepatocellular carcinoma

    doi: 10.1038/s41419-018-1281-7

    Figure Lengend Snippet: DNA methyltransferase 3B (DNMT3B) is upregulated and large tumor suppressor gene 1 (LATS1) is downregulated in hepatocellular carcinoma (HCC). a Quantitative real-time PCR (qRT-PCR) analysis of DNMT3B expression in 150 pairs of HCC tissues and paired normal adjacent tissues. b qRT-PCR analysis of LATS1 expression in 150 pairs of HCC tissues and paired normal adjacent tissues. c Immunohistochemical staining analysis of DNMT3B protein expression levels in HCC tissues. d Immunohistochemical staining analysis of LATS1 protein expression levels in HCC tissues. e Kaplan–Meier analysis of overall survival between HCC patients with high and low DNMT3B expression. f Kaplan–Meier analysis of overall survival between high and low LATS1 expression in HCC patients. g Kaplan–Meier analysis of overall survival between the high miR-29c-3p/low DNMT3B/high LATS1 expression group and low miR-29c-3p/high DNMT3B/low LATS1 expression group; ** p

    Article Snippet: Genomic DNA was isolated from HCC tumor tissues, paired normal adjacent tissues, and HCC cells using the DNA Isolation kit (Tiangen, Beijing, China) according to the manufacturer’s protocol.

    Techniques: Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Expressing, Immunohistochemistry, Staining

    Rescue experiments are performed to confirm that DNA methyltransferase 3B (DNMT3B) is the functional target of miR-29c-3p in hepatocellular carcinoma (HCC) progression. a Western blot revealed DNMT3B protein expression in MHCC-97H-miR-29c-3p cells and HepG2-miR-29c-3p that were transfected with DNMT3B vector and NC. b Proliferation of MHCC-97H-miR-29c-3p cells and HepG2-miR-29c-3p cells that were transfected with DNMT3B vector and negative control (NC) was determined by CCK-8 assay. c Wound healing assay was performed to determine the effects of DNMT3B on HCC cell migration. d Colony formation assays assessed the effects of DNMT3B on HCC cell proliferation. e The methylation status of large tumor suppressor gene 1 (LATS1) was detected in MHCC-97H-miR-29c-3p cells and HepG2-miR-29c-3p cells that were transfected with DNMT3B vector and NC. f Western blot revealed the expression of Hippo signaling pathway components, including proliferation- and apoptosis-related indicators in MHCC-97H-miR-29c-3p cells and HepG2-miR-29c-3p cells that were transfected with DNMT3B vector and NC; * p

    Journal: Cell Death & Disease

    Article Title: miR-29c-3p regulates DNMT3B and LATS1 methylation to inhibit tumor progression in hepatocellular carcinoma

    doi: 10.1038/s41419-018-1281-7

    Figure Lengend Snippet: Rescue experiments are performed to confirm that DNA methyltransferase 3B (DNMT3B) is the functional target of miR-29c-3p in hepatocellular carcinoma (HCC) progression. a Western blot revealed DNMT3B protein expression in MHCC-97H-miR-29c-3p cells and HepG2-miR-29c-3p that were transfected with DNMT3B vector and NC. b Proliferation of MHCC-97H-miR-29c-3p cells and HepG2-miR-29c-3p cells that were transfected with DNMT3B vector and negative control (NC) was determined by CCK-8 assay. c Wound healing assay was performed to determine the effects of DNMT3B on HCC cell migration. d Colony formation assays assessed the effects of DNMT3B on HCC cell proliferation. e The methylation status of large tumor suppressor gene 1 (LATS1) was detected in MHCC-97H-miR-29c-3p cells and HepG2-miR-29c-3p cells that were transfected with DNMT3B vector and NC. f Western blot revealed the expression of Hippo signaling pathway components, including proliferation- and apoptosis-related indicators in MHCC-97H-miR-29c-3p cells and HepG2-miR-29c-3p cells that were transfected with DNMT3B vector and NC; * p

    Article Snippet: Genomic DNA was isolated from HCC tumor tissues, paired normal adjacent tissues, and HCC cells using the DNA Isolation kit (Tiangen, Beijing, China) according to the manufacturer’s protocol.

    Techniques: Functional Assay, Western Blot, Expressing, Transfection, Plasmid Preparation, Negative Control, CCK-8 Assay, Wound Healing Assay, Migration, Methylation

    Aberrant DNA hypermethylation and expression of large tumor suppressor gene 1 (LATS1) in hepatocellular carcinoma (HCC) and HCC cell lines. a The methylation status of LATS1 was randomly detected in 7 HCC and paired normal adjacent tissues. b The methylation status of LATS1 was detected in LO2, MHCC-97H, HepG2, SMMC-7721, and Huh7cell lines. c Bisulfite sequencing analysis was performed on LATS1 promoter methylation in HCC tissues compared with paired normal adjacent tissues. d The relative mRNA expression of miR-29c-3p in 7 HCC and paired normal adjacent tissues. e The relative mRNA expression of DNA methyltransferase 3B (DNMT3B) in 7 HCC and paired normal adjacent tissues. f The relative mRNA expression of LATS1 in 7 HCC and paired normal adjacent tissues. g The CpG islands (shaded area) of LATS1 promoter region. h YAP and LATS1 protein expression in HCC and paired normal adjacent tissues. i YAP and LATS1 protein expression in HCC and LO2 cells; * p

    Journal: Cell Death & Disease

    Article Title: miR-29c-3p regulates DNMT3B and LATS1 methylation to inhibit tumor progression in hepatocellular carcinoma

    doi: 10.1038/s41419-018-1281-7

    Figure Lengend Snippet: Aberrant DNA hypermethylation and expression of large tumor suppressor gene 1 (LATS1) in hepatocellular carcinoma (HCC) and HCC cell lines. a The methylation status of LATS1 was randomly detected in 7 HCC and paired normal adjacent tissues. b The methylation status of LATS1 was detected in LO2, MHCC-97H, HepG2, SMMC-7721, and Huh7cell lines. c Bisulfite sequencing analysis was performed on LATS1 promoter methylation in HCC tissues compared with paired normal adjacent tissues. d The relative mRNA expression of miR-29c-3p in 7 HCC and paired normal adjacent tissues. e The relative mRNA expression of DNA methyltransferase 3B (DNMT3B) in 7 HCC and paired normal adjacent tissues. f The relative mRNA expression of LATS1 in 7 HCC and paired normal adjacent tissues. g The CpG islands (shaded area) of LATS1 promoter region. h YAP and LATS1 protein expression in HCC and paired normal adjacent tissues. i YAP and LATS1 protein expression in HCC and LO2 cells; * p

    Article Snippet: Genomic DNA was isolated from HCC tumor tissues, paired normal adjacent tissues, and HCC cells using the DNA Isolation kit (Tiangen, Beijing, China) according to the manufacturer’s protocol.

    Techniques: Expressing, Methylation, Methylation Sequencing

    ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the DNA bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence

    Journal: BMC Genomics

    Article Title: Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity

    doi: 10.1186/s12864-018-4748-0

    Figure Lengend Snippet: ) was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM of the selected effector and 25% (v/v) DMSO at 65 °C. The pictures on the right side of the figure’s panels show the theoretical arrangement of the DNA bands in an agarose gel after digesting the given substrate DNA with TthHB27I under standard conditions. a Cleavage pattern of non-methylated 1789 bp PCR fragment DNA. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder, lane K, untreated DNA; lane 1, cleavage reaction in the absence of effector and DMSO; lane 2, in the presence of DMSO only; lane 3, in the presence of SAM only; lane 4, in the presence of SAM and DMSO; lane 5, in the presence of SIN only; lane 6, in the presence of SIN and DMSO. b The same as ( a ), but with previously methylated 1789 bp PCR fragment. c The same as ( a ), but with 1850 bp PCR fragment without TthHB27I cognate recognition sequence

    Article Snippet: DNA isolation kit (GeneJet Plasmid Miniprep Kit), DNA markers (GeneRuler 1 kb DNA Ladder, 100 bp Plus DNA Ladder), SmaI REase, FastAP Thermosensitive Alkaline Phosphatase, T4 DNA Polymerase and T4 DNA Ligase were from Thermo Fisher Scientific/Fermentas (Vilnius, USA/Lithuania).

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

    Cleavage of λ DNA under TthHB27I specificity relaxation conditions. a Cleavage pattern of λ DNA digested with TthHB27I under various conditions. 0.5 μg of DNA substrate was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM SAM and/or 25% (v/v) DMSO for 4 h at 65 °C. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, digestion in the presence of SAM; lane 2, digestion in the presence of DMSO; lane 3, digestion in the presence of both SAM and DMSO. b The same as ( a ), but SIN was used instead of SAM. c Distribution of insert lengths in 200 clones randomly selected from TthHB27I/DMSO/SAM-generated λ DNA library. d The same as ( c ), but for TthHB27I/DMSO/SIN-generated λ DNA library

    Journal: BMC Genomics

    Article Title: Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity

    doi: 10.1186/s12864-018-4748-0

    Figure Lengend Snippet: Cleavage of λ DNA under TthHB27I specificity relaxation conditions. a Cleavage pattern of λ DNA digested with TthHB27I under various conditions. 0.5 μg of DNA substrate was digested with 2 U of TthHB27I in REase buffer supplemented with 100 μM SAM and/or 25% (v/v) DMSO for 4 h at 65 °C. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, digestion in the presence of SAM; lane 2, digestion in the presence of DMSO; lane 3, digestion in the presence of both SAM and DMSO. b The same as ( a ), but SIN was used instead of SAM. c Distribution of insert lengths in 200 clones randomly selected from TthHB27I/DMSO/SAM-generated λ DNA library. d The same as ( c ), but for TthHB27I/DMSO/SIN-generated λ DNA library

    Article Snippet: DNA isolation kit (GeneJet Plasmid Miniprep Kit), DNA markers (GeneRuler 1 kb DNA Ladder, 100 bp Plus DNA Ladder), SmaI REase, FastAP Thermosensitive Alkaline Phosphatase, T4 DNA Polymerase and T4 DNA Ligase were from Thermo Fisher Scientific/Fermentas (Vilnius, USA/Lithuania).

    Techniques: Clone Assay, Generated

    ) was incubated with 2 U of TthHB27I for 1 h at 65 °C in REase buffer with increasing amount of DMSO. Reaction mixtures were precipitated and electrophoresed in 1.3% agarose/TBE gels. The pictures on the right side of the figure show the theoretical arrangement of the DNA bands in an agarose gel after digesting the substrate DNA with TthHB27I under standard conditions. a Digestions performed only with the addition of DMSO, without any cofactor. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested PCR fragment; lane 1, 0% ( v /v) DMSO present in the reaction mixture; lane 2, with 5% (v/v) DMSO; lane 3, with 10% (v/v) DMSO; lane 4, with 15% (v/v) DMSO; lane 5, with 20% (v/v) DMSO; lane 6, with 25% (v/v) DMSO; lane 7, with 30% (v/v) DMSO. As in ( a ), but in the presence of 100 μM SAM ( b ); 100 μM SIN ( c ); 100 μM SAC ( d ); 100 μM SAH ( e ); 100 μM ATP ( f )

    Journal: BMC Genomics

    Article Title: Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity

    doi: 10.1186/s12864-018-4748-0

    Figure Lengend Snippet: ) was incubated with 2 U of TthHB27I for 1 h at 65 °C in REase buffer with increasing amount of DMSO. Reaction mixtures were precipitated and electrophoresed in 1.3% agarose/TBE gels. The pictures on the right side of the figure show the theoretical arrangement of the DNA bands in an agarose gel after digesting the substrate DNA with TthHB27I under standard conditions. a Digestions performed only with the addition of DMSO, without any cofactor. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested PCR fragment; lane 1, 0% ( v /v) DMSO present in the reaction mixture; lane 2, with 5% (v/v) DMSO; lane 3, with 10% (v/v) DMSO; lane 4, with 15% (v/v) DMSO; lane 5, with 20% (v/v) DMSO; lane 6, with 25% (v/v) DMSO; lane 7, with 30% (v/v) DMSO. As in ( a ), but in the presence of 100 μM SAM ( b ); 100 μM SIN ( c ); 100 μM SAC ( d ); 100 μM SAH ( e ); 100 μM ATP ( f )

    Article Snippet: DNA isolation kit (GeneJet Plasmid Miniprep Kit), DNA markers (GeneRuler 1 kb DNA Ladder, 100 bp Plus DNA Ladder), SmaI REase, FastAP Thermosensitive Alkaline Phosphatase, T4 DNA Polymerase and T4 DNA Ligase were from Thermo Fisher Scientific/Fermentas (Vilnius, USA/Lithuania).

    Techniques: Incubation, Agarose Gel Electrophoresis, Polymerase Chain Reaction

    Controlling of partial cleavage of genomic DNAs by TthHB27I under cofactor/analogue-induced ‘star’ activity conditions. E. coli and λ genomic DNAs were digested with TthHB27I under cofactor/analogue-induced ‘star’ conditions, while varying: temperature, incubation time and TthHB27I amount. 0.5 μg of DNAs were digested with TthHB27I in REase buffer supplemented with 100 μM SIN and 25% (v/v) DMSO. a Cleavage control by reaction temperature. Reactions conducted with E. coli DNA digested with 2 U of TthHB27I for 1 h at temperatures from 30 °C to 80 °C. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, reaction at 30 °C; lane 2, 35 °C; lane 3, 40 °C; lane 4, 45 °C; lane 5, 50 °C; lane 6, 55 °C; lane 7, 60 °C; lane 8, 65 °C; lane 9, 70 °C; lane 10, 75 °C; lane 11, 80 °C. b The same as ( a ), except that λ DNA was used. c Cleavage control by reaction time. E. coli DNA was digested at 65 °C at times ranging from 7.5 min to 16 h. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, reaction conducted for 7.5 min; lane 2, 15 min; lane 3, 30 min; lane 4, 1 h; lane 5, 2 h; lane 6, 4 h; lane 7, 8 h; lane 8, 16 h. d The same as ( c ), except that λ DNA was used. e Cleavage control by the enzyme amount. E. coli DNA was digested at 65 °C with TthHB27I. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, DNA digested with 8 U TthHB27I; lane 2, 4 U; lane 3, 2 U; lane 4, 1 U; lane 5, 0.5 U; lane 6, 0.25 U; lane 7, 0.12 U; lane 8, 0.06 U. f The same as ( e ), except that λ DNA was used

    Journal: BMC Genomics

    Article Title: Randomized DNA libraries construction tool: a new 3-bp ‘frequent cutter’ TthHB27I/sinefungin endonuclease with chemically-induced specificity

    doi: 10.1186/s12864-018-4748-0

    Figure Lengend Snippet: Controlling of partial cleavage of genomic DNAs by TthHB27I under cofactor/analogue-induced ‘star’ activity conditions. E. coli and λ genomic DNAs were digested with TthHB27I under cofactor/analogue-induced ‘star’ conditions, while varying: temperature, incubation time and TthHB27I amount. 0.5 μg of DNAs were digested with TthHB27I in REase buffer supplemented with 100 μM SIN and 25% (v/v) DMSO. a Cleavage control by reaction temperature. Reactions conducted with E. coli DNA digested with 2 U of TthHB27I for 1 h at temperatures from 30 °C to 80 °C. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, reaction at 30 °C; lane 2, 35 °C; lane 3, 40 °C; lane 4, 45 °C; lane 5, 50 °C; lane 6, 55 °C; lane 7, 60 °C; lane 8, 65 °C; lane 9, 70 °C; lane 10, 75 °C; lane 11, 80 °C. b The same as ( a ), except that λ DNA was used. c Cleavage control by reaction time. E. coli DNA was digested at 65 °C at times ranging from 7.5 min to 16 h. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, reaction conducted for 7.5 min; lane 2, 15 min; lane 3, 30 min; lane 4, 1 h; lane 5, 2 h; lane 6, 4 h; lane 7, 8 h; lane 8, 16 h. d The same as ( c ), except that λ DNA was used. e Cleavage control by the enzyme amount. E. coli DNA was digested at 65 °C with TthHB27I. Lane M1, GeneRuler 1 kb DNA Ladder; lane M2, 100 bp Plus DNA Ladder; lane K, undigested DNA; lane 1, DNA digested with 8 U TthHB27I; lane 2, 4 U; lane 3, 2 U; lane 4, 1 U; lane 5, 0.5 U; lane 6, 0.25 U; lane 7, 0.12 U; lane 8, 0.06 U. f The same as ( e ), except that λ DNA was used

    Article Snippet: DNA isolation kit (GeneJet Plasmid Miniprep Kit), DNA markers (GeneRuler 1 kb DNA Ladder, 100 bp Plus DNA Ladder), SmaI REase, FastAP Thermosensitive Alkaline Phosphatase, T4 DNA Polymerase and T4 DNA Ligase were from Thermo Fisher Scientific/Fermentas (Vilnius, USA/Lithuania).

    Techniques: Activity Assay, Incubation