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Sample GSM5321304 Query DataSets for GSM5321304
Status Public on Jan 16, 2024
Title Td_c
Sample type SRA
Source name Mouse Liver
Organism Mus musculus
Characteristics cell type: liver
Treatment protocol 1.ATAC-seq was applied to 293T, HeLa, HepG2 and MCF7 cell line. 2.ATAC-seq was applied to mouse liver rhythm model.3. ChIP-seq was applied to different cells with different treatment.
Growth protocol Cell lines 293T were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and Pen-Strep (100 U / ml penicillin, 100 mg / ml streptomycin) at 37℃, 5% CO2.
Extracted molecule genomic DNA
Extraction protocol Cells were harvested and wash once with cold 1x PBS buffer, and then resuspended in 1 mL cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 1mM PMSF). This cell lysis reaction was incubated on ice for 10 min.
DNA libraries were prepared for sequencing using TruePrepTM DNA Library Prep Kit V2 for Illumina().
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
Description We designed and expressed a novel Tn5-dCas9 fusion protein to perform ATAC-seq. Td represents Tn5-dCas9. sg means ATAC-seq with targeted sgRNA. c represented ATAC-seq with control sgRNA.
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 or mm10 whole genome using bowtie2 v2.2.6 with parameters with the parameters -X2000 and -m1.
Remove mitochondrial DNA with
Peak calling with macs2 v 2.2.1
Motif finding with homer(
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: narrowPeak files were generated using macs2
Submission date May 18, 2021
Last update date Jan 16, 2024
Contact name Haizhu Zhang
Phone 18621062295
Organization name Fudan University
Department Institutes of Biomedical Sciences
Lab He Fuchu Lab
Street address No. 131 Dong'an Road, Xuhui District
City Shanghai
ZIP/Postal code 200032
Country China
Platform ID GPL24247
Series (2)
GSE174642 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon (various cell lines II)
GSE174643 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon
BioSample SAMN19243591
SRA SRX10921866

Supplementary file Size Download File type/resource
GSM5321304_R21047290-Td-c-Td-c_atac.narrowPeak.gz 3.1 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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