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Sample GSM1167210 Query DataSets for GSM1167210
Status Public on Sep 05, 2013
Title LHX2_ChIPSeq_replicate1
Sample type SRA
Source name Mouse back skins
Organism Mus musculus
Characteristics gender: Female
age: P52-60
strain: CD-1
sorting markers: integrin α6 and CD34
chip antibody: LHX2
Treatment protocol No treatment
Growth protocol HFSCs were purifed by FACS from the backskins of mice
Extracted molecule genomic DNA
Extraction protocol Sorted cells were crosslinked by addition of 1/10th volume of fresh 11% formaldehyde solution. Before ChIP, cells were resuspended, lysed, and sonicated to solubilize and shear crosslinked DNAs. The resulting whole-cell extract was incubated LHX2 antibody. After ChIP, samples were washed with low salt, high salt, LiCl, and Tris-EDTA buffer. Bound complexes were eluted and crosslinking was reversed.
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 Genome Analyzer IIx
Description Chromatin IP against LHX2
Data processing bam files created using bowtie 0.12.7 allowing for only unique reads with 2 mismatches over 36bp
wig files created using igvtools with 100bp extension from bam files using mm9
Submission date Jun 18, 2013
Last update date May 15, 2019
Contact name Alicia Rodriguez-Folgueras
Organization name Rockefeller University
Street address 1230 York Ave.
City New York
ZIP/Postal code 10065
Country USA
Platform ID GPL11002
Series (1)
GSE48068 Architectural niche organization by LHX2 is linked to hair follicle stem cell function
BioSample SAMN02207980
SRA SRX310225

Supplementary file Size Download File type/resource
GSM1167210_Lhx2_replicate_1_bowtie.bam.wig.gz 21.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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