|
| Status |
Public on Nov 13, 2019 |
| Title |
ATAC-Seq Sample_DMSO_sg6_KO_2 |
| Sample type |
SRA |
| |
|
| Source name |
Breast Cancer Cell
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
treatment: DMSO
sgguide: sgARID1A-3
genotype: ARID1A KO
|
| Treatment protocol |
MCF7 cells were treated with DMSO of Fulvestrant (100nM) for 24 hours.
|
| Growth protocol |
MCF7 cells were obtained from ATCC and were cultured in DMEM/F-12 (Corning) and supplemented with 10% FBS, MEM non-essential amino acids (Corning), 50U/ml penicillin, and 50ng/ml streptomycin under normal oxygen conditions (5% CO2, 37 °C)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed as described by Buenrostro et al, 2013 with the exception that 0.2% NP40 was used for cell lysis.
ATAC-seq libraries were prepared using Illumina's TruSeq ChIP sample prep.Libraries were validated using the Agient Technologies 2100 Bioanalyzer and Qubit high sensitivity assay.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw reads were trimmed using trimmomatic (v0.35, Parameters: TruSeq3-PE adapters, LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Each sample was aligned to hg38 genome using bowtie2 (v2.2.6, Parameters: -X2000 –local –mm --no-mixed --no-discordant).
Duplicate reads were then removed using MarkDuplicates (v2.9.0, REMOVE_DUPLICATES=True).
In order to account for Tn5 shift, all positive strand reads in each sample were shifted by +4bps and all negative strand reads were shifted by -5bps.
Peak calling was first performed on after pooling all samples using MACS2 (v2.1.0, parameters: --nomodel --extsize 150 --shift -75 --slocal 5000 --llocal 20000 -B --keep-dup all -p 0.05) and then on individual samples (-p 0.01).
BigWig tracks were generated using MACS2 and then scaled using rtracklayer (v1.40.6).
Genome_build: hg38
Supplementary_files_format_and_content: normalized bw files
|
| |
|
| Submission date |
Dec 20, 2018 |
| Last update date |
Nov 15, 2019 |
| Contact name |
Sagar Chhangawala |
| E-mail(s) |
sagar.cornell@gmail.com
|
| Organization name |
Weill Cornell Medical College
|
| Department |
PBSB
|
| Street address |
1300 York Ave.
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE124224 |
ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer (ATAC-Seq) |
| GSE124228 |
ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer |
|
| Relations |
| BioSample |
SAMN10621798 |
| SRA |
SRX5172050 |
