NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3605270 Query DataSets for GSM3605270
Status Public on Jul 11, 2019
Title ESC_EpiLC_exp1_cell104
Sample type SRA
 
Source name cultured mESC_EpiLC
Organism Mus musculus
Characteristics strain: C57BL/6
fixed by: formaldehyde
cell type: cultured mESC_EpiLC
chip antibody: H3K27ac, Abcam, ab4729, Lot: GR3205526-1
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 Crosslinked cells were treated with 0.3% SDS at 37°C and followed by gentle sonication. Transposition was set up by incubation at 37°C for 1 h, followed by addition of stopping buffer. Soluble chromatin was used for following ChIP experiments. DNA was eluted from beads, reverse crosslinked and treated with proteinase K. Finally, DNA was extracted by pheno-chloroform.
After PCR enrichment using NEBNext Q5 Ultra II 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 HiSeq 2500
 
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 "-N 1".
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 bed files of non-duplicated reads.
 
Submission date Feb 14, 2019
Last update date Jul 11, 2019
Contact name Chen Li
E-mail(s) chenli_imm@pku.edu.cn
Organization name Peking University
Department Institute of Molecular Medicine
Lab Aibin He Lab
Street address Yihe Yuan Road No.5
City Beijing
State/province Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL17021
Series (2)
GSE109762 Profiling chromatin state by single-cell itChIP-seq
GSE126572 Profiling chromatin state by single-cell itChIP-seq [ESC_EpiLC]
Relations
BioSample SAMN10936673
SRA SRX5377043

Supplementary file Size Download File type/resource
GSM3605270_ESC_EpiLC_exp1_cell104.bed.gz 46.1 Kb (ftp)(http) BED
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