|
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.
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|
|
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 |