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Sample GSM1705261 Query DataSets for GSM1705261
Status Public on Nov 21, 2015
Title Primed_H3K27ac_R2
Sample type SRA
 
Source name Embryonic stem cells
Organism Homo sapiens
Characteristics cell type: Primed
chip antibody: H3K27Ac
antibody manufacturer: Abcam
antibody catalog: ab4729
young_id: 20150206_3645
system: Embryo
Treatment protocol None
Growth protocol Primed hESCs were cultured as previously described (Theunissen et al., 2014). Primed hESCs were maintained on mitomycin C-inactivated MEF feeder layers and passaged every 7-10 days. When passaging primed hESCs, clumps of cells were partially dissociated with collagenase type IV (GIBCO, 17104-019), and then subjected to two sedimentation steps in stationary 50 cm tubes for 10 minutes at room temperature in primed hESC medium to remove single cells. Primed hESC medium (500 ml) consisted of 400 ml of Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F12, Invitrogen, 11320), 75 ml Fetal Bovine Serum (FBS, Hyclone, SH30071.03HI), 25 ml KnockOutTM Serum Replacement (KSR, Invitrogen, 10828-028), supplemented with 1 mM glutamine (Invitrogen, 25030-024), 1% nonessential amino acids (Invitrogen, 11140-050), penicillin-streptomycin (Invitrogen, 15140-122), 0.1 mM β- mercaptoethanol (Sigma, M6250-100ML), and 4 ng/ml FGF2 (R&D systems, 233-FB- 025).
Extracted molecule genomic DNA
Extraction protocol Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
genome build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1
 
Submission date Jun 08, 2015
Last update date May 15, 2019
Contact name Richard A Young
E-mail(s) young_computation@wi.mit.edu
Phone 617-258-5219
Organization name Whitehead Institute for Biomedical Research
Lab Young Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (2)
GSE69646 3D Chromosome Regulatory Landscape of Human Pluripotent Cells [ChIP-Seq]
GSE69647 3D Chromosome Regulatory Landscape of Human Pluripotent Cells
Relations
BioSample SAMN03764719
SRA SRX1053372

Supplementary file Size Download File type/resource
GSM1705261_20150206_3645.4512.rpm.WIG.gz 92.2 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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