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sequencing libraries  (TaKaRa)


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    TaKaRa sequencing libraries
    Sequencing Libraries, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 589 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/thruplex+dna+seq+libraries/pm41663397-430-0-11?v=TaKaRa
    Average 96 stars, based on 589 article reviews
    sequencing libraries - by Bioz Stars, 2026-07
    96/100 stars

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    (A,B) Profile plot of H3K36me1 counts per million (CPM) normalized read density (NRD) through the promoter region (−3kB to TSS) of genes in H2030-BrM3 cells, under control (A) or cluster forming (B) conditions and categorized by levels of gene expression. mRNA levels were scaled on expression in H2030-BrM3 control or cluster forming conditions taken at Day 5 ranging from unexpressed (Unex.) < Tertile 1 (T1) < Tertile 2 (T2) < Tertile 1 (T3). Number of genes per tertile are: N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control and N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) for clusters. Traces show average of n=4 biological replicates. (C) Box- and-Whisker plots of NRD of traces for A and B. P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0059), T0 cluster vs. T3 control (p=0.0022), T0 control vs. T1 control (p=0.0039), and T2 cluster vs. T3 cluster (p=0.0007). (D,E) Quantification of H3K36me1 (D) or H3K36me2 (E) NRD in H2030-BrM3 clusters with the indicated shRNAs through the promoter of activated regions. N=105 loci. P-values by Wilcoxon matched-pairs test. (F,G) Quantification as in D,E, but in 3kB regions surrounding CpG islands genome-wide. N= 20,079 Me1 shControl, 22,200 me1 shKDM2A-1, 24,440 me2 shCon, 23,306 me2 shKdm2a-1. P-values by Wilcoxon matched-pairs test only on those loci with coverage in both conditions. (H) Profile plot of H3K36me1/2/3 average enrichment in KDM2A target genes that are activated (left) or suppressed (right) in H2030-BrM3 clusters. Traces are average of N=4 biological replicates collected at Day 5. (I) Comparative quantification of the promoter region (−3.0 Kb to TSS) for genes from both groups plotted in D. P-value by Mann-Whitney. (J) IGV tracks of CPM NRD for the KDM2A activated gene CYC1 with annotation of CGI, KDM2A chromatin binding peaks, and H3K36me1 peaks in shCon and shKDM2A-1 expressing H2030-BrM3 clusters. Traces are average of n=2 for FLAG-KDM2A and N=4 for <t>H3K36</t> biological replicates.
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    (A,B) Profile plot of H3K36me1 counts per million (CPM) normalized read density (NRD) through the promoter region (−3kB to TSS) of genes in H2030-BrM3 cells, under control (A) or cluster forming (B) conditions and categorized by levels of gene expression. mRNA levels were scaled on expression in H2030-BrM3 control or cluster forming conditions taken at Day 5 ranging from unexpressed (Unex.) < Tertile 1 (T1) < Tertile 2 (T2) < Tertile 1 (T3). Number of genes per tertile are: N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control and N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) for clusters. Traces show average of n=4 biological replicates. (C) Box- and-Whisker plots of NRD of traces for A and B. P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0059), T0 cluster vs. T3 control (p=0.0022), T0 control vs. T1 control (p=0.0039), and T2 cluster vs. T3 cluster (p=0.0007). (D,E) Quantification of H3K36me1 (D) or H3K36me2 (E) NRD in H2030-BrM3 clusters with the indicated shRNAs through the promoter of activated regions. N=105 loci. P-values by Wilcoxon matched-pairs test. (F,G) Quantification as in D,E, but in 3kB regions surrounding CpG islands genome-wide. N= 20,079 Me1 shControl, 22,200 me1 shKDM2A-1, 24,440 me2 shCon, 23,306 me2 shKdm2a-1. P-values by Wilcoxon matched-pairs test only on those loci with coverage in both conditions. (H) Profile plot of H3K36me1/2/3 average enrichment in KDM2A target genes that are activated (left) or suppressed (right) in H2030-BrM3 clusters. Traces are average of N=4 biological replicates collected at Day 5. (I) Comparative quantification of the promoter region (−3.0 Kb to TSS) for genes from both groups plotted in D. P-value by Mann-Whitney. (J) IGV tracks of CPM NRD for the KDM2A activated gene CYC1 with annotation of CGI, KDM2A chromatin binding peaks, and H3K36me1 peaks in shCon and shKDM2A-1 expressing H2030-BrM3 clusters. Traces are average of n=2 for FLAG-KDM2A and N=4 for <t>H3K36</t> biological replicates.
    Library Preparation, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    (A,B) Profile plot of H3K36me1 counts per million (CPM) normalized read density (NRD) through the promoter region (−3kB to TSS) of genes in H2030-BrM3 cells, under control (A) or cluster forming (B) conditions and categorized by levels of gene expression. mRNA levels were scaled on expression in H2030-BrM3 control or cluster forming conditions taken at Day 5 ranging from unexpressed (Unex.) < Tertile 1 (T1) < Tertile 2 (T2) < Tertile 1 (T3). Number of genes per tertile are: N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control and N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) for clusters. Traces show average of n=4 biological replicates. (C) Box- and-Whisker plots of NRD of traces for A and B. P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0059), T0 cluster vs. T3 control (p=0.0022), T0 control vs. T1 control (p=0.0039), and T2 cluster vs. T3 cluster (p=0.0007). (D,E) Quantification of H3K36me1 (D) or H3K36me2 (E) NRD in H2030-BrM3 clusters with the indicated shRNAs through the promoter of activated regions. N=105 loci. P-values by Wilcoxon matched-pairs test. (F,G) Quantification as in D,E, but in 3kB regions surrounding CpG islands genome-wide. N= 20,079 Me1 shControl, 22,200 me1 shKDM2A-1, 24,440 me2 shCon, 23,306 me2 shKdm2a-1. P-values by Wilcoxon matched-pairs test only on those loci with coverage in both conditions. (H) Profile plot of H3K36me1/2/3 average enrichment in KDM2A target genes that are activated (left) or suppressed (right) in H2030-BrM3 clusters. Traces are average of N=4 biological replicates collected at Day 5. (I) Comparative quantification of the promoter region (−3.0 Kb to TSS) for genes from both groups plotted in D. P-value by Mann-Whitney. (J) IGV tracks of CPM NRD for the KDM2A activated gene CYC1 with annotation of CGI, KDM2A chromatin binding peaks, and H3K36me1 peaks in shCon and shKDM2A-1 expressing H2030-BrM3 clusters. Traces are average of n=2 for FLAG-KDM2A and N=4 for <t>H3K36</t> biological replicates.
    Dna Libraries Forngswere Obtainedwith Thethruplex Dna Seq Kit, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/thruplex+dna+seq+libraries/pm41168166-309-0-6?v=TaKaRa
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    Image Search Results


    (A,B) Profile plot of H3K36me1 counts per million (CPM) normalized read density (NRD) through the promoter region (−3kB to TSS) of genes in H2030-BrM3 cells, under control (A) or cluster forming (B) conditions and categorized by levels of gene expression. mRNA levels were scaled on expression in H2030-BrM3 control or cluster forming conditions taken at Day 5 ranging from unexpressed (Unex.) < Tertile 1 (T1) < Tertile 2 (T2) < Tertile 1 (T3). Number of genes per tertile are: N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control and N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) for clusters. Traces show average of n=4 biological replicates. (C) Box- and-Whisker plots of NRD of traces for A and B. P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0059), T0 cluster vs. T3 control (p=0.0022), T0 control vs. T1 control (p=0.0039), and T2 cluster vs. T3 cluster (p=0.0007). (D,E) Quantification of H3K36me1 (D) or H3K36me2 (E) NRD in H2030-BrM3 clusters with the indicated shRNAs through the promoter of activated regions. N=105 loci. P-values by Wilcoxon matched-pairs test. (F,G) Quantification as in D,E, but in 3kB regions surrounding CpG islands genome-wide. N= 20,079 Me1 shControl, 22,200 me1 shKDM2A-1, 24,440 me2 shCon, 23,306 me2 shKdm2a-1. P-values by Wilcoxon matched-pairs test only on those loci with coverage in both conditions. (H) Profile plot of H3K36me1/2/3 average enrichment in KDM2A target genes that are activated (left) or suppressed (right) in H2030-BrM3 clusters. Traces are average of N=4 biological replicates collected at Day 5. (I) Comparative quantification of the promoter region (−3.0 Kb to TSS) for genes from both groups plotted in D. P-value by Mann-Whitney. (J) IGV tracks of CPM NRD for the KDM2A activated gene CYC1 with annotation of CGI, KDM2A chromatin binding peaks, and H3K36me1 peaks in shCon and shKDM2A-1 expressing H2030-BrM3 clusters. Traces are average of n=2 for FLAG-KDM2A and N=4 for H3K36 biological replicates.

    Journal: bioRxiv

    Article Title: Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A

    doi: 10.64898/2026.01.22.701120

    Figure Lengend Snippet: (A,B) Profile plot of H3K36me1 counts per million (CPM) normalized read density (NRD) through the promoter region (−3kB to TSS) of genes in H2030-BrM3 cells, under control (A) or cluster forming (B) conditions and categorized by levels of gene expression. mRNA levels were scaled on expression in H2030-BrM3 control or cluster forming conditions taken at Day 5 ranging from unexpressed (Unex.) < Tertile 1 (T1) < Tertile 2 (T2) < Tertile 1 (T3). Number of genes per tertile are: N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control and N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) for clusters. Traces show average of n=4 biological replicates. (C) Box- and-Whisker plots of NRD of traces for A and B. P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0059), T0 cluster vs. T3 control (p=0.0022), T0 control vs. T1 control (p=0.0039), and T2 cluster vs. T3 cluster (p=0.0007). (D,E) Quantification of H3K36me1 (D) or H3K36me2 (E) NRD in H2030-BrM3 clusters with the indicated shRNAs through the promoter of activated regions. N=105 loci. P-values by Wilcoxon matched-pairs test. (F,G) Quantification as in D,E, but in 3kB regions surrounding CpG islands genome-wide. N= 20,079 Me1 shControl, 22,200 me1 shKDM2A-1, 24,440 me2 shCon, 23,306 me2 shKdm2a-1. P-values by Wilcoxon matched-pairs test only on those loci with coverage in both conditions. (H) Profile plot of H3K36me1/2/3 average enrichment in KDM2A target genes that are activated (left) or suppressed (right) in H2030-BrM3 clusters. Traces are average of N=4 biological replicates collected at Day 5. (I) Comparative quantification of the promoter region (−3.0 Kb to TSS) for genes from both groups plotted in D. P-value by Mann-Whitney. (J) IGV tracks of CPM NRD for the KDM2A activated gene CYC1 with annotation of CGI, KDM2A chromatin binding peaks, and H3K36me1 peaks in shCon and shKDM2A-1 expressing H2030-BrM3 clusters. Traces are average of n=2 for FLAG-KDM2A and N=4 for H3K36 biological replicates.

    Article Snippet: In brief, samples were checked by Agilent Bioanalyzer, and libraries were prepared by the using ThruPlex DNA Seq (Takara Bio. cat. R400674) for H3K36 libraries, and DNA SMART ChiP-Seq (Takara Bio.cat.

    Techniques: Control, Gene Expression, Expressing, Whisker Assay, Genome Wide, MANN-WHITNEY, Binding Assay

    (A) Normalized read density (NRD) of H3K27Ac through the promoter region (−3kB to TSS) of genes in H2030-BrM3 cell clusters categorized by tertile of expression as in . N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) genes. Traces show average of 3 biological replicates taken at Day 5 after seeding in cluster forming conditions. (B) Profile plot of H3K36me2 CPM NRD as in . N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) genes. (C) Box-and-Whisker plots of NRD for traces underlying B and control conditions (data not shown). P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0025) and T0 control vs T1 control (p=0.5792). N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control. (D) Profile plot of H3K36me3 NRD as in (B) N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) genes. (E) Box-and-Whisker plots of NRD for traces underlying D and control conditions (data not shown). P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0992), T0 control vs. T1 control (p=0.5396), T0 control vs. T2 cluster (p=0.9180), T1 control vs. T2 cluster (p>0.9999), and T2 control vs. T3 cluster (p>0.9999). N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control. (F) Total protein levels of histone H3 and the indicated H3K36 modifications in shCon and shKDM2A H2030-BrM3 clusters +/− Dox for 5 days. (G) Proportion of peak summits annotated by HOMER to promoter, intergenic, intronic, exonic, or transcription termination site (TTS) regions in control or tumor cell cluster conditions. Proportions represent the average of peaks across N=4 biological replicates at Day 5 after. (H) IGV tracks of CPM NRD for the KDM2A suppressed gene ABCA5 , with annotation of CGI, KDM2A chromatin binding peaks, and H3K36me1/2 peaks in shCon and shKDM2A-1 expressing H2030-BrM3 clusters. Traces are average of N=2 for FLAG-KDM2A and N=4 for H3K36 biological replicates.

    Journal: bioRxiv

    Article Title: Tumor Cell Clustering Enhances Metastatic Competence by Regulating the H3K36 Histone Demethylase KDM2A

    doi: 10.64898/2026.01.22.701120

    Figure Lengend Snippet: (A) Normalized read density (NRD) of H3K27Ac through the promoter region (−3kB to TSS) of genes in H2030-BrM3 cell clusters categorized by tertile of expression as in . N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) genes. Traces show average of 3 biological replicates taken at Day 5 after seeding in cluster forming conditions. (B) Profile plot of H3K36me2 CPM NRD as in . N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) genes. (C) Box-and-Whisker plots of NRD for traces underlying B and control conditions (data not shown). P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0025) and T0 control vs T1 control (p=0.5792). N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control. (D) Profile plot of H3K36me3 NRD as in (B) N=4163 Unex., 5219 (T1), 5235 (T2), 5219 (T3) genes. (E) Box-and-Whisker plots of NRD for traces underlying D and control conditions (data not shown). P-value by Kruskal-Wallis test with all comparisons p<0.0001 using Dunn’s multiple testing correction except: T0 cluster vs. T1 cluster (p=0.0992), T0 control vs. T1 control (p=0.5396), T0 control vs. T2 cluster (p=0.9180), T1 control vs. T2 cluster (p>0.9999), and T2 control vs. T3 cluster (p>0.9999). N=3642 (Unex.), 5397 (T1), 5398 (T2), and 5399 (T3) for control. (F) Total protein levels of histone H3 and the indicated H3K36 modifications in shCon and shKDM2A H2030-BrM3 clusters +/− Dox for 5 days. (G) Proportion of peak summits annotated by HOMER to promoter, intergenic, intronic, exonic, or transcription termination site (TTS) regions in control or tumor cell cluster conditions. Proportions represent the average of peaks across N=4 biological replicates at Day 5 after. (H) IGV tracks of CPM NRD for the KDM2A suppressed gene ABCA5 , with annotation of CGI, KDM2A chromatin binding peaks, and H3K36me1/2 peaks in shCon and shKDM2A-1 expressing H2030-BrM3 clusters. Traces are average of N=2 for FLAG-KDM2A and N=4 for H3K36 biological replicates.

    Article Snippet: In brief, samples were checked by Agilent Bioanalyzer, and libraries were prepared by the using ThruPlex DNA Seq (Takara Bio. cat. R400674) for H3K36 libraries, and DNA SMART ChiP-Seq (Takara Bio.cat.

    Techniques: Expressing, Whisker Assay, Control, Binding Assay