SS18-SSX2 ChIP-seq data

Published: 11 June 2024| Version 2 | DOI: 10.17632/7mhyv8f6vp.2
Yanfeng Zhang


Flag-SSX ChIP-seq and Input read coverage data in bdg format, Peak data. The ChIP-seq data are processed as follows: The raw ChIP-seq data (FASTQ format) were first adaptor-trimmed, then mapped to the human reference genome (hg19) using Bowtie2 program (version 2.1.0) with the default setting. After removing duplicated reads, we used the MACS2 (version 2.1) software to identify peaks using the matched DNA input data as the control. Based on the coordinate of called peaks, the overlap rate between two TF binding peaks was analyzed using the Bedtools program. The peaks were ranked by the number of mapped reads within the peak interval and the top 10% of peaks were selected for motif discovery. The summits of the top 10% peaks were extended by 100 bp on either side. Motifs between 5 and 30 bp in length were identified on both strands. We employed the MEME 4.9.1 toolkit to search DNA motifs and enrichment significance for candidate TFs.