|
| Status |
Public on Dec 19, 2016 |
| Title |
MCF10a_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
mammary epithelial cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF10a
cell type: mammary epithelial cell line
cell status: Healthy cells with passage number < 30
|
| Treatment protocol |
baseline
|
| Growth protocol |
MCF10A cells were cultured in Dulbecco’s modified Eagle’s medium DMEM (Invitrogen) with 5% horse serum (Invitrogen), 1% penicillin/streptomycin (Invitrogen), 20 ng/ml EGF (Peprotech), 0.5 μg/ml hydrocortisone(Sigma), 100 ng/ml cholera toxin (Sigma) and 10 μg/ml insulin (Sigma) . Cells were grown in a humidified incubator at 37°C with 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell lysis in hypotonic solution
nextera kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
library strategy: ATAC-seq
Align with bowtie2
Merge bam files for all replicates
Normalize and create BedGraph, bigWig
Peak calling with hotspot (standard paramters)
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph and bigWig file for merged replicates, hotspot file with spots calculated by hotspot with fdr <0.01
|
| |
|
| Submission date |
Oct 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Guertin |
| E-mail(s) |
guertin@virginia.edu
|
| Organization name |
University Of Virginia
|
| Street address |
1340 Jefferson Park Ave
|
| City |
Charlottesville |
| State/province |
Virginia |
| ZIP/Postal code |
22908 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE89013 |
Identification of Breast Cancer Associated Variants That Modulate Transcription Factor Binding |
|
| Relations |
| BioSample |
SAMN05932793 |
| SRA |
SRX2255549 |
