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Sample GSM2229388 Query DataSets for GSM2229388
Status Public on Aug 02, 2016
Title H3K27ac_TKO3a1-r2
Sample type SRA
 
Source name Embryonic stem cell (ESC)
Organism Mus musculus
Characteristics cell type: ESC
line: C57BL/6
genotype: TKO+Dnmt3a1
antibody: H3K27ac (Active Motif 39133)
Growth protocol Mouse embryonic stem cells (mESCs) were grown on irradiated mouse embryonic fibroblasts and maintained in DMEM supplemented with 15% fetal bovine serum, 1 mM GlutaMAX, 1X Non-essential amino acids, 1X Penicillin/Streptomycin, mLIF, and 0.001% β-mercaptoethanol.
Extracted molecule genomic DNA
Extraction protocol mESCs were pre-plated to deplete MEF feeders before collection. Cells were fixed with 1% formaldehyde after which chromatin was isolated and sonicated to 150-300 bp using Bioruptor (Diagenode). Sonicated chromatin was precleared with Protein A/G Dynabeads then incubated in antibody overnight. Chromatin was then immunoprecipitated with Protein A/G Dynabeads for > 2 hours. ChIP was washed successively by two rounds of low-salt buffer, two rounds of high-salt buffer, two rounds of LiCl buffer, and finally two rounds of TE buffer. ChIP DNA was eluted in TE, reverse crosslinked overnight, treated with RNase A, then proteinase K, and finally extracted with phenol-chloroform and ethanol precipitation.
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit per manufacturer's recommendations. Libraries were quantified using Qubit Fluorometer and Bioanalyzer High Sensitivity DNA Analysis Kit individually. Libraries were pooled and sequenced using the Illumina HiSeq 2000 machine as either 50-bp or 100-bp single-end sequencing reads.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing Fastq files were demultiplexed and generated using bcl2fastq version 1.8.4
Reads were mapped to mm9 genome using bowtie version 1.1.0 with options -m1 --best -v2
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph data displays ChIP-seq sequencing reads normalized to a depth of 1e7. Each read is extended by the predicted sequencing fragment length.
 
Submission date Jul 09, 2016
Last update date May 15, 2019
Contact name Andrew King
E-mail(s) andking@ucla.edu
Phone 310-266-7009
Organization name UCLA
Department Human Genetics
Lab Guoping Fan
Street address Gonda Bldg Rm. 6554, P.O.Box 957088
City Los Angeles
State/province CA
ZIP/Postal code 90095-7088
Country USA
 
Platform ID GPL21103
Series (2)
GSE77002 Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Embryonic Stem Cells (ChIP-seq)
GSE77004 Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Embryonic Stem Cells
Relations
BioSample SAMN05370087
SRA SRX1922262

Supplementary file Size Download File type/resource
GSM2229388_K27ac_TKO3a1-r2.bedGraph.gz 127.3 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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