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Protocol publication

[…] rcinoma cell lines. NUP210 was the only gene not showing the dual modifications in either SAEC or another normal cell line, Normal adult Human Lung Fibroblasts (NHLF). It was also one of the two genes showing aberrant overexpression among all 26 lung adenocarcinoma cell lines compared to the normal cell line SAEC, although the extent of overexpression was usually smaller in the other paired datasets. The results indicate that NUP210 gene is the most promising epigenetic biomarker for lung adenocarcinoma., We used ChIP-seq data of 26 lung adenocarcinoma cell lines and SAEC from the DBTSS database () []. To identify the regions of histone modifications, “peaks” of ChIP-Seq tags were called by MACS2 for the six types of histone modifications (H3K27ac, H3K4me3, H3K4me1, H3K9me3, H3K36me3, and H3K27me3) in each cell line. Narrow peaks (H3K27ac, H3K4me3, and H3K4me1) were detected by MACS2 with default options. Broad peaks (H3K9me3, H3K36me3, and H3K27me3) were detected by MACS2 using “-broad” and “-nomodel” options [] and specifying “-q (q-value)” to be 0.05 according to the official website of MACS (https://github.com/taoliu/MACS/)., For each lung adenocarcinoma cell line, we extracted histone modifications that were not detected in SAEC. From the histone modifications, we calculated frequency of shared histone modifications among the 26 lung adenocarcinoma cell lines (as a population) by bedtools version 2.22.1 []. These histone modifications were annotated in terms of closest genes and distances to Transcriptional Start Sites (TSS) of the genes by the package of ChIPseeker [] in R version 3.1.0 when they were found in ≥85% (22 out of 26) among the lung adenocarcinoma cell lines. We focused on genes with the histone modification in their promoters defined as up to ±1.5 kb from the most upstream TSSs []., We examined ChIP-Seq data of NHLF, another only one normal lung cell line for which ChIP-Seq experiments have been conducted and their peaks were inferred and made publicly available by Bernstein–Broad Institute (http://genome-mirror.duhs.duke.edu/ENCODE/cellTypes.html). We examined whether the histone modifications for genes of interest in lung adenocarcinoma cell lines are also absent in NHLF cells., We examined the expression levels of genes of in […]

Pipeline specifications

Software tools MACS, BEDTools, ChIPseeker
Diseases Neoplasms