GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM3711216 Query DataSets for GSM3711216
Status Public on Jul 15, 2019
Title H3K27ac_2K_ESC_rep1
Sample type SRA
Source name H3K27ac_2K_ESC
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: native, cultured mESC (V6.5)
chip antibody: H3K27ac, Abcam, ab4729, Lot: GR3211959-1
Growth protocol Mouse embryonic stem cells were cultured in DMEM/F12 and neurobasal with 2i or 15% fetal bovine serum
Extracted molecule genomic DNA
Extraction protocol The ESC was dissociated by 0.1% Trypsin digestion, and aliquot of cell numbers were directly used for in-situ ChIP
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NovaSeq 6000
Data processing Basecalls performed using CASAVA version 1.8.2.
Sequenced reads were trimmed and filtered by cutadapt (v 1.11) to get high quality reads.
High quality reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Peaks were called by MACS2 (v 2.1.1), with parameter of "--broad"
Bigwig files were generated from bam files using deeptools (v 2.2.3) bamCoverage. All samples were normalized to 10 million reads with binsize as 50 bp by “--scaleFactor, --binSize 50” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files. Bigwig files of replicates data show reproducbility.
Submission date Apr 04, 2019
Last update date Jul 15, 2019
Contact name Haiqing Xiong
Organization name Peking University
Street address 5 Yiheyuan Road, Haidian District
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
Platform ID GPL24247
Series (2)
GSE129333 CoBATCH for high-throughput single-cell epigenomic profiling [low input in situ ChIP]
GSE129335 CoBATCH for high-throughput single-cell epigenomic profiling
BioSample SAMN11340698
SRA SRX5637720

Supplementary file Size Download File type/resource 27.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap