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Sample GSM953076 Query DataSets for GSM953076
Status Public on Jun 04, 2013
Title Mouse heart doxorubicin FAIRE-seq
Sample type SRA
Source name mouse heart
Organism Mus musculus
Characteristics cell type: mouse heart cells
treatment: 10 mg/kg doxorubicin
time point: 4 hours post treatment
strain: FVB nude
age: 10 weeks
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-enriched DNA
Data processing Reads were aligned to mm9 using BWA, duplicates and reads with mapping quality less than 37 were removed.
Peaks: Peak regions were called by using F-seq package.
Genome_build: mm9
Supplementary_files_format_and_content: bed files indicate the peak regions.
Submission date Jun 27, 2012
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 GPL13112
Series (2)
GSE33632 Genome-wide analysis of histone eviction by FAIRE-Seq
GSE33634 Topoisomerase II inhibitors and histone eviction
SRA SRX156323
BioSample SAMN01081703

Supplementary file Size Download File type/resource
GSM953076.bed.gz 1.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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