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Pipeline publication

[…] varis S220 followed by shearing to 100-800 bp in protease inhibitor-containing lysis buffer, according to the Nexon protocol []. Sheared chromatins were precipitated with the H3K9me2 antibody ab1220 (Abcam), reversed cross-linked, proteinase K-treated and DNA purified., The immunoprecipitated and purified HCT116 genomic DNA, including the input DNA as control, were used for library preparation with Illumina TrueSeq reagents. To verify the size of PCR enriched fragments, the template size distribution was analyzed on a DNA1000 chip in a 2100 Bioanalyzer (Agilent Technologies). Sequencing reads were generated on the Illumina HiSeq2500 platform. Single-end raw reads were trimmed (Q30), mapped (BWA read mapping), and subject to duplicate reads removal (Picard), peak calling (MACS), and peak annotation (SnpEff) for downstream analysis., We thank Sanford D. Markowitz for kindly providing genomic DNA from MSI+ CRC cell lines., Author contributions , T.P. designed the study, conducted experiments, analyzed data and wrote the paper. V.R. conducted experiments, analyzed data and wrote the paper. J.L., C.L., J.L., I.S. and S.K. conducted experiments and analyzed data. M.A.A. provided vectors and advice for generation of the targeting construct. L.H. analyzed RNA-seq data. M.H. designed in-vivo experiments. A.L. designed ChIP experiments and analyzed data. T.S. designed the study, analyzed data and wrote the paper. All authors read and commented on the manuscript and finally approved it., CONFLI […]

Pipeline specifications

Software tools BWA, Picard, SnpEff
Organisms Homo sapiens
Diseases Neoplasms, Gastrointestinal Neoplasms, Digestive System Neoplasms, Intestinal Diseases, Genomic Instability
Chemicals Nucleotides