|
| Status |
Public on May 31, 2018 |
| Title |
MDA-MB-231 PVT1 targeting sgRNA R3 rep2 |
| Sample type |
SRA |
| |
|
| Source name |
MDA-MB-231 clonal cell line expressing dCas9-BFP-KRAB construct
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
|
| Treatment protocol |
For MDA-MB-231 or MCF7 cell line, lentivirus harboring mU6-sgRNA (control or PVT1 R2/R3). Selected by Puromycin 1 ug/ml for 4 days. Recovered for one day in media without Puromycin.
|
| Growth protocol |
For MDA-MB231 and MCF7 cell line, Cultured in DMEM supplemented with 10% FBS + 1% pen-strep. HCT116 cell line was maintained with Mcoy's 5A media supplemented with 10% FBS + 1% pen-strep
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Qiagen MinElute column
Standard ATAC-seq protocol.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Basecalls
Trimming for Nextseq adaptor
Align using Bowtie2
Removing dupulicate using Picard
Peak calling using MACS2
Genome_build: Hg19
Supplementary_files_format_and_content: MACS2 output describing peak region and count
|
| |
|
| Submission date |
Apr 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Howard Y. Chang |
| E-mail(s) |
howchang@stanford.edu
|
| Phone |
650-725-7022
|
| Organization name |
Stanford
|
| Lab |
Chang Lab
|
| Street address |
269 Campus Drive, CCSR 2130
|
| City |
Stanford |
| State/province |
CALIFORNIA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE97583 |
Next Generation Sequencing for Chromatin accessbility by ATAC-seq for MDA-MB-231, MCF7 or HCT116 cell line |
| GSE97669 |
Promoter of lncRNA gene *PVT1* is a tumor suppressor DNA element |
|
| Relations |
| BioSample |
SAMN06705671 |
| SRA |
SRX2731925 |
