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Sample GSM2966530 Query DataSets for GSM2966530
Status Public on Jul 11, 2019
Title ATAC-50K-ESC_rep2
Sample type SRA
Source name ATAC-50K-ESC
Organism Mus musculus
Characteristics strain: C57BL/6
cell type: cultured native mouse embryonic stem cell (mESC)
Growth protocol Mouse embryonic stem cells were cultured in DMEM/F12 with 2i or 15% fetal bovine serum.
Extracted molecule genomic DNA
Extraction protocol Native cells were collected for 50,000 each group. Cells were lysed gently and tagmented by Tn5-MEA/B. After tagmentation, adaptor-ligated DNA was immediately extracted using QIAGEN QIAquick kit.
DNA was amplified for 14 cycles with NEBNext Q5 Ultra II master mix. The desirable size range was 200-800 bp, size-selected using AMPure XP beads. The sequencing strategy was on HiSeq 4000, for paired end 150 bp.
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
Description Transposase-accessible chromatin
Data processing Basecalls performed using CASAVA version 1.8.2.
ATAC-seq 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.
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 data files were bigwig files. Bigwig files showed the signal of reads distribution, reflecting the enrichment of open chromatin regions got from ATAC-seq.
Submission date Jan 29, 2018
Last update date Jul 11, 2019
Contact name Chen Li
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)
GSE109760 Profiling chromatin state by single-cell itChIP-seq [ATAC-seq]
GSE109762 Profiling chromatin state by single-cell itChIP-seq
BioSample SAMN08427384
SRA SRX3606378

Supplementary file Size Download File type/resource 85.6 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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