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GEO help: Mouse over screen elements for information. |
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Status |
Public on Aug 02, 2016 |
Title |
H3K27ac_TKO |
Sample type |
SRA |
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Source name |
Embryonic stem cell (ESC)
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Organism |
Mus musculus |
Characteristics |
cell type: ESC line: C57BL/6 genotype: TKO antibody: H3K27ac (Active Motif 39133)
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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.
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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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.
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Submission date |
Jul 09, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Andrew King |
E-mail(s) |
andking@ucla.edu
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Phone |
310-266-7009
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Organization name |
UCLA
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Department |
Human Genetics
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Lab |
Guoping Fan
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Street address |
Gonda Bldg Rm. 6554, P.O.Box 957088
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City |
Los Angeles |
State/province |
CA |
ZIP/Postal code |
90095-7088 |
Country |
USA |
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Platform ID |
GPL13112 |
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 |
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Relations |
BioSample |
SAMN05370085 |
SRA |
SRX1922260 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2229386_K27ac_TKO.bedGraph.gz |
134.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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