NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE142809 Query DataSets for GSE142809
Status Public on Dec 16, 2020
Title CRISPRi screen of prostate cancer associated risk cis-regulatory elements [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Prostate cancer (PCa) associated risk SNPs are enriched in cis-regulatory elements (CREs). In this study, we screened 260 CREs that contain at least one PCa risk SNP for essentiality in V16A, 22Rv1 and A549 cells. We tiled the CREs and 14 control regions using 5,873 sgRNAs.
 
Overall design A pooled library of cells lacking individial CREs or control regions was generated using CRISPR/dCas9-KRAB suppression technique. The regions were targeted using a custom sgRNA library. The cell DNA were extracted at day 0 and day 16, and the abundance of sgRNA was estimated using NGS.
 
Contributor(s) He HH
Citation(s) 33741908
Submission date Jan 01, 2020
Last update date Apr 20, 2021
Contact name Musaddeque Ahmed
E-mail(s) musaddeque.ahmed@gmail.com
Organization name University health Network
Lab He Lab
Street address 101 College St
City Toronto
State/province ON
ZIP/Postal code M5G1L7
Country Canada
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (12)
GSM4240438 sgLac_-_V16A [sgCtr1]
GSM4240439 sgLacZ_-_22RV1 [sgCtr1]
GSM4240440 sgLuc_-_22RV1 [sgCtr2]
This SubSeries is part of SuperSeries:
GSE142811 CRISPRi screen of prostate cancer associated risk cis-regulatory elements
Relations
BioProject PRJNA598431
SRA SRP239223

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
GSE142809_RNAseq_22rv1_count_matrix.txt.gz 268.8 Kb (ftp)(http) TXT
GSE142809_RNAseq_V16A_count_matrix.txt.gz 261.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap