|
| Status |
Public on Jan 16, 2024 |
| Title |
MCF7 ATAC-seq |
| Sample type |
SRA |
| |
|
| Source name |
MCF7 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: MCF7
|
| 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 |
| |
|
| 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 removeChrom.py
Peak calling with macs2 v 2.2.1
Motif finding with homer(findMotifsGenome.pl)
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 |
| E-mail(s) |
zhz2230@qq.com
|
| 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 |
GPL24676 |
| 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 |
|
| Relations |
| BioSample |
SAMN19243564 |
| SRA |
SRX10921863 |
