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Sample GSM2966501 Query DataSets for GSM2966501
Status Public on Jul 11, 2019
Title H3K4me3_1M-sonication-ChIP-ESC_rep1
Sample type SRA
 
Source name H3K4me3_1M-sonication-ChIP-ESC
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: cultured mESC
fixed by: formaldehyde for 3 min
chip antibody: H3K4me3, Millipore, 04-745, Lot: 2872328, 1.5 μg added
Growth protocol Mouse embryonic stem cells were cultured in DMEM/F12 with 2i or 15% fetal bovine serum, and MEFs in DMEM medium with 10% fetal bovine serum.
Extracted molecule genomic DNA
Extraction protocol Crosslinked cells were lysed and sonciated to 200-800 bp fragments. Soluble chromatin was used for ChIP experiments. DNA on beads were tagmented with Tn5 transposome following the Nextera protocol.
After PCR enrichment using NEBNext Q5 Ultra II master mix, products were purified and size selected by AMPure XP beads for 200-1000 bp.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
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 samtools (v 1.3.1) rmdup.
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 1 bp by “--scaleFactor, --binSize 1” parameters.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bigwig files. Bigwig files of sonication-ChIP showed the enriched signal of H3K4me3 across the whole genome. They were positive controls, approving that itChIP-seq did a better job.
 
Submission date Jan 29, 2018
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 GPL21103
Series (2)
GSE109759 Profiling chromatin state by single-cell itChIP-seq [sonication ChIP]
GSE109762 Profiling chromatin state by single-cell itChIP-seq
Relations
BioSample SAMN08427388
SRA SRX3606374

Supplementary file Size Download File type/resource
GSM2966501_H3K4me3_1M-sonication-ChIP-ESC_rep1.bw 389.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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