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Sample GSM958501 Query DataSets for GSM958501
Status Public on Jul 20, 2012
Title H2AZ_mES_ChIPSeq
Sample type SRA
 
Source name H2AZ_mES_ChIPSeq
Organism Mus musculus
Characteristics cell type: Pluripotent embryonic stem cells
passage: passage 5-10
chip antibody: H2A.Z (Millipore 07-594)
strain: 129SVJae x C57BL6
Growth protocol Mouse v6.5 ES cells were cultured on fibroblast feeders in DMEM (Sigma) with 15% fetal bovine serum (Hyclone), GlutaMax (Invitrogen), MEM non-essential amino acids (Invitrogen), pen/strep (Invitrogen), ESGRO (Chemicon) and 2-mercaptoethanol (Sigma), incubating at 37oC, 5% CO2 [16]. Prior to harvest, these cells were passaged 2-3 times on feeder-free gelatinized tissue culture plates.
Mouse NP cells were generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).
Human H1 ES cells were cultured in TeSR media on Matrigel by Cellular Dynamics International. Cells were split with dispase and harvested at a passage number between 30 and 40. Prior to harvest, cells were karyotyped and stained for Oct4 to confirm pluripotency.
Extracted molecule genomic DNA
Extraction protocol Lysates were clarified from sonicated nuclei and histone-DNA or protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. 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 (32 to 52 exo minus) 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 15 cycles and library fragments of ~250 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 Illumina Genome Analyzer or HiSeq following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description v6.5- mouse embryonic stem cells
Data processing ChIP-Seq reads for mouse and human were aligned to reference assemblies mm8 and hg18, respectively.
Bowtie version 0.12.8 was used with the default parameters, with reads discarded if they aligned to more than 10 places.
To create density files, the reads were extended to 200 bp and converted to BigWig using BedTools and UCSC wigToBigWig.
Supplementary_files_format_and_content: BigWig files containing the read densities for all regions.
 
Submission date Jul 10, 2012
Last update date May 15, 2019
Contact name Bradley E. Bernstein
E-mail bernstein.bradley@mgh.harvard.edu
Phone 617-726-6906
Fax 617-643-3566
Organization name Massachusetts General Hospital
Street address 185 Cambridge Street, CPZN 8234
City Boston
State/province MA
ZIP/Postal code 02114
Country USA
 
Platform ID GPL9185
Series (1)
GSE39237 H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions
Relations
SRA SRX159082
BioSample SAMN01086967

Supplementary file Size Download File type/resource
GSM958501_mES_H2AZ_mm8.nodup.sorted.bw 53.9 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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