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Sample GSM1502005 Query DataSets for GSM1502005
Status Public on Mar 19, 2015
Title HFSC_invitro_H3K27ac_ChIP-seq
Sample type SRA
 
Source name primary HFSCs
Organism Mus musculus
Characteristics gender: Female
passage: 7
strain: K14-H2B-iRFP
sorting markers: integrin α6, CD34 and Sca1, iRFP
chip antibody: H3K27ac (abcam, catalog# ab4729, lot# GR132150-1)
cell type: cultured HFSCs
Treatment protocol No treatment
Growth protocol HFSCs and TACs were FACS-purifed from the back skins of indicated ages of mice
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of 150-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chromatin IP against H3K27ac
Data processing Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification.
Peak detection was performed with the software MACS (Version 1.4.2) with input as controls.
wig files created using IGVtools with 25bp windows with no extension to reads.
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows
 
Submission date Sep 10, 2014
Last update date May 15, 2019
Contact name Rene Christian Adam
Organization name Regeneron Pharmaceuticals
Street address 777 Old Saw Mill River Road
City Tarrytown
State/province New York
ZIP/Postal code 10591
Country USA
 
Platform ID GPL13112
Series (1)
GSE61316 Pioneer factors govern super-enhancer dynamics in stem cell plasticity and lineage choice
Relations
BioSample SAMN03031679
SRA SRX699297

Supplementary file Size Download File type/resource
GSM1502005_HFSC_invitro-H3K27ac-ChIP_NoIndex_L002_R1_001.wig.gz 45.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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