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Series GSE97583 Query DataSets for GSE97583
Status Public on May 31, 2018
Title Next Generation Sequencing for Chromatin accessbility by ATAC-seq for MDA-MB-231, MCF7 or HCT116 cell line
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary CRISPRi on PVT1 did not induce drastic changes on chromatin accessbility in MDA-MB-231 cell line. CCAT1 enhancer is accessble specifically in HCT116, not in MCF7 or MDA-MB-231.
 
Overall design MDA-MB-231 cell line was treated non-targeting control sgRNA or PVT1 targeting sgRNA. All cell lines express dCas9-BFP-KRAB integrated via lentivirus.
 
Contributor(s) Cho SW, Chang HY
Citation(s) 29731168
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
 
Platforms (2)
GPL15520 Illumina MiSeq (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (10)
GSM2572559 MDA-MB-231 control sgRNA rep1
GSM2572560 MDA-MB-231 control sgRNA rep2
GSM2572561 MDA-MB-231 PVT1 targeting sgRNA R2 rep1
This SubSeries is part of SuperSeries:
GSE97669 Promoter of lncRNA gene *PVT1* is a tumor suppressor DNA element
Relations
BioProject PRJNA382394
SRA SRP103775

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE97583_RAW.tar 6.6 Mb (http)(custom) TAR (of NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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