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Sample GSM831860 Query DataSets for GSM831860
Status Public on Jun 04, 2013
Title SW620 un-treated FAIRE-seq
Sample type SRA
Source name SW620 cells
Organism Homo sapiens
Characteristics cell type: Human colon adenocarcinoma
cell line: SW620
treatment: Un-treated
time point: control
Treatment protocol Tissue culture cells were treated with indicated drugs for 4 hours then fixed and collected for processing. Mice were injected iv with a single dose of the indicated drugs and 4 hours later, tissues were fixed and collected for processing.
Growth protocol Tissue culture cells were grown in 15cm dishes around 80% confluency.
Extracted molecule genomic DNA
Extraction protocol After fixation, lysates were cleared from sonicated nuclei and histone-free DNA were isolated by phenol-chloroform extraction. Libraries were prepared according to the provider’s kits and protocols for ChIP samples.
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
Description FAIRE-seq
Data processing Reads were aligned to hg19 using BWA, duplicates and reads with mapping quality less than 60 were removed.
Peaks: Peak regions were called by using F-seq package.
Submission date Nov 11, 2011
Last update date May 15, 2019
Contact name Baoxu Pang
Organization name Stanford University
Department Genetics
Lab Michael Snyder
Street address 3165 Porter Drive
City Palo Alto
State/province CALIFORNIA
ZIP/Postal code 94304
Country USA
Platform ID GPL11154
Series (2)
GSE33632 Genome-wide analysis of histone eviction by FAIRE-Seq
GSE33634 Topoisomerase II inhibitors and histone eviction
SRA SRX105583
BioSample SAMN00754048

Supplementary file Size Download File type/resource
GSM831860_SW620_FAIRE_Untreated_fseqpeaks.bed.gz 374.6 Kb (ftp)(http) BED
GSM831860_SW620_FAIRE_Untreated_uniq-q37.bam 887.9 Mb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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