|Public on Apr 05, 2017
|cell type: hTERT immortalized endometriosis cells
genotype/variation: ARID1A Knockdown
|Nuclei were fixed, lysed, and chromatin was sonicated. Histone-DNA complexes were isolated with antibody. Genomic DNA was isolated by standard phenol-chloroform extraction and ethanol precipitation
Libraries were prepared according to Illumina's instructions and sequenced on either HiSeq-2000 or NextSeq 500 platforms.
|Illumina NextSeq 500
|ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Non-unique reads were filtered out and reads were mapped to hg19 using BWA
Reads were extended to 200bp, duplicates removed.
Peaks were called using MACS algorithm with a p-value cut-off of 10^-10. Read-count quantification was perfomed then log2 transformed -- corrected for total read count of the largest datastore, only reads within peaks were counted, and corrected for peak length.
Supplementary_files_format_and_content: Text files with peak list and read-count quantification
|Sep 12, 2016
|Last update date
|May 15, 2019
|University of Southern California
|1441 Eastlake ave NOR7336
|Genome-wide histone modification profiling in endometriosis cells