|
| Status |
Public on Oct 30, 2019 |
| Title |
MCF7-ARID1A_KO_Clone_11_Vehicle rep 4 |
| Sample type |
SRA |
| |
|
| Source name |
MCF7-ARID1A_KO_Clone_11_ATAC-seq_Vehicle
|
| Organism |
Homo sapiens |
| Characteristics |
genotype/variation: MCF7 ARID1A knockout clone 11
cell type: ER+ Breast Cancer Cell Line
passages: 35-45
treatment: Vehicle
|
| Treatment protocol |
Cells were treated with vehicle (DMSO) or 100 nM 4-Hydroxytamoxifen for 6 hours.
|
| Growth protocol |
MCF7 cells were grown in DMEM High glucose media with 2 mM Glutamine, 10% FBS, Sodium pyruvate
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Omni ATAC-seq protocol was performed from Corces et al., 2017, Nature Methods. Transposase and buffers were purchased from Illumina Nextera kits.
DNA was prepared for Illumina sequencing using Nextera indices on the HiSeq 4000 with paired end 150 bp.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
mcf7_arid1a_ko_clone_11_veh_c11.macs2.bed.gz
mcf7_arid1a_ko_clone_11_veh_c11.genrich.bed.gz
|
| Data processing |
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library.
The peaks were called with MACS2, version 2.1.1.20160309, using following parameters: -g hs -f BAM --nomodel --shift -100 --extsize 200.
For estimation of consistency in results of peak calling we used also Genrich, version 0.5, with parameters: -j -y -r -v.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: hg38
Supplementary_files_format_and_content: bed/text
|
| |
|
| Submission date |
Jul 15, 2019 |
| Last update date |
Oct 30, 2019 |
| Contact name |
Jason Carroll |
| E-mail(s) |
Jason.Carroll@cruk.cam.ac.uk
|
| Phone |
+44 1223 769649
|
| Organization name |
Cancer Research UK, Cambridge Institute
|
| Street address |
Li Ka Shing Centre, Robinson Way
|
| City |
Cambridge |
| ZIP/Postal code |
CB2 ORE |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE123286 |
ARID1A and the BAF complex are determinants of breast cancer treatment response |
| GSE134270 |
ARID1A and the BAF complex are determinants of breast cancer treatment response [ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN12275845 |
| SRA |
SRX6443499 |
