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Sample GSM7789743 Query DataSets for GSM7789743
Status Public on Jun 24, 2024
Title ESC_rep3
Sample type SRA
Source name MEF
Organism Mus musculus
Characteristics cell line: MEF
cell type: Mouse embryonic fibroblast
Extracted molecule genomic DNA
Extraction protocol DNA was harvested using TruePrep DNA Library Prep Kit V2 for Illumina kit (TD501-TD503, Vazyme),100000 cells per sample was used for sequencing libraries construction
Liarbries were constructed by TruePrep DNA Library Prep Kit V2 for Illumina (TD501-TD503, Vazyme)
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Data processing ATAC-seq was performed according to the previous study (Buenrostro et al., 2013, Buenrostro et al., 2015a). Briefly, a total of 50,000 cells were collected and incubated with 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630) for 10 min on ice. The suspension of nuclei was centrifuged for 5 min at 500g at 4 °C, then resuspended in 50 μl transposition reaction mix (10 μl 5× TTBL, 5 μl TTE Mix V50 and 35 μl nuclease-free H2O) from the TruePrep DNA Library Prep Kit V2 for Illumina (TD501-TD503, Vazyme), and incubated at 37 °C for 30 min. DNA fragments were then PCR amplified and purified with a Qiaquick PCR (QIAGEN) column. Library concentration was detected by a VAHTS Human Genomic DNA Quantification and QC Kit (NQ201, Vazyme) according to the manufacturer’s protocol. Finally, libraries were indexed using TruePrep Index Kit V2 for Illumina (Vazyme, TD202), and sequencing was performed on Illumina Novaseq PE150 platform.
The ATAC-seq reads were trimmed by Trim Galore (v0.6.4) and then mapped to the mm10 reference genome using bowtie2 (v2.4.5), and SAMtools (v1.16.1) was used to remove the repetitive, low sequencing quality (mapq<30) and the mitochondrial DNA mapped reads in the total mapped reads. In order to make the data comparable between different sequencing depths, the signals were normalized to one million reads for each sample, and the value were further compressed into a binary format (bigWig) for downstream analysis and data visualization. Peak calling was performed using MACS (v1.4.2) with parameters as follows: -g mm --keep-dup all --nomodel --shiftsize 25.
Assembly: mm10
Supplementary files format and content: BigWig, Peaks&Summits bed
Submission date Sep 19, 2023
Last update date Jun 24, 2024
Contact name Chengchen Zhao
Organization name Westlake University
Lab Laboratory of Cell Fate Control
Street address Dunyu Road No.600, Xihu District
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310030
Country China
Platform ID GPL24247
Series (2)
GSE243513 Rational cell fate engineering through chromatin dynamics [ATAC-Seq]
GSE243517 Rational cell fate engineering through chromatin dynamics
BioSample SAMN37452919
SRA SRX21820607

Supplementary file Size Download File type/resource 126.5 Mb (ftp)(http) BW
GSM7789743_ESC_3.peaks.bed.gz 1.3 Mb (ftp)(http) BED
GSM7789743_ESC_3.summits.bed.gz 985.8 Kb (ftp)(http) BED
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