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Sample GSM1890754 Query DataSets for GSM1890754
Status Public on Jan 26, 2016
Title LS180_H3K27ac
Sample type SRA
 
Source name LS-180
Organism Homo sapiens
Characteristics cimp status: CIMP (-)
chip antibody: H3K27ac
cell line: LS-180
Treatment protocol None
Growth protocol Cell lines were grown at 37 degrees celsius and crosslinked for ChIP during logarithmic growth phase.
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde for 15 minutes (Brd4 ChIP) or 5 minutes (H3K27ac ChIP). DNA was sonicated to an average length of 200 - 500 bp. IP and Input DNA was reverse crosslinked and purified for library preparation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description H3K27ac ChIP
Data processing Reads were aligned to the human genome (hg19) using the BWA algorithm (default settings).
Duplicate reads were removed and only uniquely mapped reads (mapping quality >= 25) were used for further analysis.
For Brd4 ChIP-seq, samples were normalized using Drosophila chromatin spike-in. Briefly, normalization was performed by equalizing the Drosophila tag counts across all samples so that the final tag counts were based off of the sample containing the lowest number of Drosophila tags. Then the human tags counts for all samples were proportionally scaled based on the ratios used to adjust the drosophila tag counts. Scaling to the target tag number was performed by randomly removing excess tags. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome to generate bigWig files.
For H3K27ac ChIP-seq, samples were normalized by random downsampling to a specific number of total reads and bedgraph files were generated using Bedtools (default settings).
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files, bigWig files
 
Submission date Sep 22, 2015
Last update date May 15, 2019
Contact name Florian Gnad
Organization name Genentech
Street address 1 DNA Way
City South San Francisco
ZIP/Postal code 94080
Country USA
 
Platform ID GPL18573
Series (1)
GSE73319 CCAT1 is a cMYC super-enhancer templated RNA that predicts BET sensitivity in cancer
Relations
BioSample SAMN04100875
SRA SRX1272804

Supplementary file Size Download File type/resource
GSM1890754_LS180_H3K27Ac_i83_15M.bedgraph.gz 123.8 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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