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Sample GSM2308944 Query DataSets for GSM2308944
Status Public on Apr 05, 2017
Title KD2_H3K4me1
Sample type SRA
 
Source name Endometriosis
Organism Homo sapiens
Characteristics cell type: hTERT immortalized endometriosis cells
genotype/variation: ARID1A Knockdown
antibody: H3K4me1
Extracted molecule genomic DNA
Extraction protocol 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.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing 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.
Genome_build: hg19
Supplementary_files_format_and_content: Text files with peak list and read-count quantification
 
Submission date Sep 12, 2016
Last update date May 15, 2019
Contact name Ranjani Lakshminarasimhan
E-mail(s) ranjanil@usc.edu
Phone 3238650736
Organization name University of Southern California
Department Urology
Lab Jones/Liang
Street address 1441 Eastlake ave NOR7336
City Los Angeles
State/province California
ZIP/Postal code 90033
Country USA
 
Platform ID GPL18573
Series (1)
GSE86810 Genome-wide histone modification profiling in endometriosis cells
Relations
BioSample SAMN05762546
SRA SRX2158976

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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