nextflex dna barcoded adapters  (Bioo Scientific)

Journal: Nucleic Acids Research

Article Title: STAG2 loss-of-function affects short-range genomic contacts and modulates the basal-luminal transcriptional program of bladder cancer cells

doi: 10.1093/nar/gkab864

Figure Lengend Snippet: Rewiring of chromatin looping arising from loss of STAG2 results in transcriptional changes. ( A ) Heatmap representing the statistical significance (FDR) of motif analyses of promoters of differentially expressed genes and genomic positions involved in differential DNA looping in STAG2-silenced cells. We identify three collections of motifs: #1, motifs enriched in differential interactions; #2, motifs enriched in differentially expressed genes; and #3, motifs enriched in both interactions and transcriptionally deregulated genes. ( B ) Average fold change in gene expression values (FPKM) of genes engaged by control and differential interactions overlapping promoters or ( C ) gene bodies. Boxplot notches represent the confidence interval around the median. t -test: * P < 0.05; ** P < 0.01; *** P < 0.001. ( D , E ) Hi-C contact matrices at the TNC and COL17A1 loci in control and STAG2-silenced cells. The contact matrices for the STAG2 -silenced condition are the result of averaging the matrices for sh1 and sh2. Snapshots of the ChIP-Seq tracks for STAG1 and STAG2, differential contact matrices, H3K27me3 peaks, and gene expression values (FPKM) are included. Loss of interactions overlapping the promoter of TNC and COL17A1 upon STAG2 silencing correlates with a consistent increase in gene expression. Error bars represent mean ± SEM.

Article Snippet: The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes, Bioo Scientific, ref. 514120) using T4 DNA Ligase.

Techniques: Gene Expression, Control, Hi-C, ChIP-sequencing