|
| Status |
Public on Oct 15, 2019 |
| Title |
MCF7-ATAC-shNR2F2 |
| Sample type |
SRA |
| |
|
| Source name |
Breast
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF7
cell type: breast cancer cell line
genotype/variation: shNR2F2
|
| Treatment protocol |
DNA of MCF-7 cells with WT and NR2F2 KO were extracted using standard Illumina protocals.
|
| Growth protocol |
The MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovinw serum at 37℃ incubator
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 sorted cells were washed with cold PBS and suspended in lysis buffer for 10-15 min on ice. DNA was purified using MinElute PCR Purification Kit (Qiagen). Transposed DNA was amplified using NEB Next High-Fidelity 2X PCR Master Mix and libraries were sequenced on HiSeq 4000
DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Reads were filtered with trimmomatic (version 0.32).
Bowtie version 2.2.4 was used to align the reads against the hg19 reference genome.
Samtools 1.9 to remove PCR duplicates
MACS2 to do peak calling on all files
Genome_build: hg19
Supplementary_files_format_and_content: wig and peak files for each sample
|
| |
|
| Submission date |
Jun 10, 2019 |
| Last update date |
Oct 15, 2019 |
| Contact name |
Guojuan Jiang |
| E-mail(s) |
[email protected]
|
| Phone |
18817821244
|
| Organization name |
Shanghai Jiaotong University
|
| Department |
School of Medicine
|
| Lab |
State Key Laboratory of Medical Genomics
|
| Street address |
Ruijin er road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200025 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (2) |
| GSE132434 |
Genome-wide maps of chromatin accessibility before and after NR2F2 knock down using ATAC-seq. |
| GSE132436 |
NR2F2 study |
|
| Relations |
| BioSample |
SAMN11999181 |
| SRA |
SRX6027765 |
