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Sample GSM3936832 Query DataSets for GSM3936832
Status Public on Jan 16, 2024
Title MCF7-4HT ATAC-seq
Sample type SRA
Source name MCF7 cells
Organism Homo sapiens
Characteristics cell line: MCF7
treatment: 2 uM 4-hydroxytamoxifen(4-HT)
Treatment protocol 1.Final concentration of 20 ng/mL TNF-α was added into the cell culture medium and HeLa cells were incubated in 37 °C for 15 min, 30 min and 60 min. Cells were harvested in cold 1x PBS buffer and counted.
2.When the density of MCF7 cells was up to 70%, DMEM was changed to Phenol Red-free DMEM with 2.5% FBS for 24 h and then Phenol Red-free DMEM only for 24 h. Final concentration of 100 nM 17β-estradiol(E2) and 2 uM 4-hydroxytamoxifen(4-HT) were added into the cell culture medium, cells were incubated in 37 °C for 2 h. Cells were harvested in cold 1x PBS buffer and counted.
Growth protocol Human cell lines HeLa, HepG2 and MCF-7 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. Mouse C2C12 were cultured in DMEM supplemented with 10% FBS, 2 mM -glutamine, 100 U/ml penicillin and 100 g of streptomycin (1% Pen/Strep) at 37℃, 5% CO2. For myogenic differentiation, cells were shifted to DMEM containing 2% horse serum (differentiation medium).
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 HiSeq X Ten
Description 4HT_FKDL190738026-1a
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 Jul 10, 2019
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 GPL20795
Series (2)
GSE134086 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon (various cell lines I)
GSE174643 Proteome-wide profiling of Transcriptional Machinery on Accessible Chromatin by biotinylated transposon
BioSample SAMN12249521
SRA SRX6427768

Supplementary file Size Download File type/resource
GSM3936832_4HT.peak_peaks.narrowPeak.gz 197.6 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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