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Sample GSM3604833 Query DataSets for GSM3604833
Status Public on Jul 11, 2019
Title E8.25_heart_cell60
Sample type SRA
 
Source name heart
Organism Mus musculus
Characteristics strain: C57BL/6
age: E8.25
cell type: heart cell
chip antibody: H3K27ac, Abcam, ab4729, Lot: GR3205526-1
Growth protocol Mice were housed under a 12-12-hour light-dark cycle and allowed standard laboratory take care.
Extracted molecule genomic DNA
Extraction protocol Crosslinked cells were treated with 0.3% SDS at 62°C. Transposition was set up by incubation at 55°C for 30 min, 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
GSE126561 Profiling chromatin state by single-cell itChIP-seq [E7.75_E8.25_heart]
Relations
BioSample SAMN10935572
SRA SRX5375352

Supplementary file Size Download File type/resource
GSM3604833_E8.25_heart_cell60.bed.gz 4.1 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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