Computational protocol: Histone lysine methyltransferase G9a is a novel epigenetic target for the treatment of hepatocellular carcinoma

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Protocol publication

[…] ChIP sequencing (ChIP-Seq) was also performed as previously described []. In brief, 1 × 107 Huh7 cells were subjected to immunoprecipited using anti-H3K9me2 (Millipore, Billerica, MA) antibodies. To evaluate the histone modification H3K9me2 in each gene, normalized tag numbers in the region from 2 kb upstream to 2 kb downstream of the transcription start site (TSS) were separated by reads per million (RPM) mapped reads of the corresponding input. The RPM values of the sequenced read were calculated using BEDTools to visualize with Integrative Genomics Viewer (http://www.broadinstitute.org/igv). […]

Pipeline specifications

Software tools BEDTools, IGV
Application ChIP-seq analysis
Organisms Mus musculus
Diseases Diabetes Mellitus, Carcinoma, Hepatocellular, Neoplasms