|
| Status |
Public on Dec 01, 2023 |
| Title |
MCF10A_WT_rep1_ATAC |
| Sample type |
SRA |
| |
|
| Source name |
Breast Epithelium
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Breast Epithelium
cell line: MCF-10A
genotype: WT
|
| Growth protocol |
All cell lines were grown in 5% CO2 at 37oC with 1% Pen Strep in respective media conditions. MCF-10A parental cell lines were purchased from American Type Culture Collection (ATCC). MCF-10A cell line knock-ins were previously generated as described in Gustin et al. Parental MCF-10A cell lines were cultured in DMEM/F12 (1:1) supplemented with 5% horse serum, 20 ng/ml epidermal growth factor (EGF), 10 µg/ml insulin (Roche), 0.5 µg/mL hydrocortisone (Sigma), and 100 ng/ml cholera toxin (Sigma). Knock-in cell lines were maintained in the same conditions except without EGF. Cells were grown to 80% confluence. Twenty-four hours prior to collection of RNA or nuclei, for RNA-seq or ATAC-seq respectively, all MCF-10A cells were transferred to an assay media of phenol red-free DMEM/F12 (1:1) supplemented with 1% charcoal-dextran stripped FBS (Fisher), 0.2 ng/ml EGF, 10 µg/ml insulin, 0.5 µg/mL hydrocortisone, and 100 ng/ml cholera toxin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated and ATAC-seq libraries were prepared using previously published methods from Barnett et al 2020 Mol Cell.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MCF10A_WT_calledPeaks.narrowPeak
|
| Data processing |
All sequencing library reads were trimmed of adapters and assessed for quality using the Trim Galore! (version 0.4.0) Wrapper of Cutadapt and FastQC.
Trimmed reads were mapped to the human genome assembly hg38 using the BBTools (version 38.69) package and Burrows-Wheeler Aligner (version 0.7.17)
Quality filtering was performed on the mapped reads using SAMtools(26). Peaks of accessibility were called using Genrich (version 0.6.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing genomic coordinates of called accessible regions
|
| |
|
| Submission date |
Nov 15, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Adam Xavier Miranda |
| E-mail(s) |
adam.x.miranda@vanderbilt.edu
|
| Phone |
7045169891
|
| Organization name |
Vanderbilt University
|
| Street address |
2220 Pierce Avenue
|
| City |
Nashville |
| State/province |
TN |
| ZIP/Postal code |
37013 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE247821 |
A functional genomics process for systematic dissection and mutation-specific target discovery in breast cancer PIK3CA hotspot mutations [ATAC-Seq] |
| GSE247822 |
A functional genomics process for systematic dissection and mutation-specific target discovery in breast cancer PIK3CA hotspot mutations |
|
| Relations |
| BioSample |
SAMN38266061 |
| SRA |
SRX22534010 |
