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Series GSE219166 Query DataSets for GSE219166
Status Public on Mar 09, 2023
Title CRISPR screens identify gene targets at breast cancer risk loci [RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Genome-wide association studies (GWAS) have identified >200 loci associated with breast cancer (BC) risk. The majority of candidate causal variants (CCVs) are in non-coding regions and likely modulate cancer risk by regulating gene expression. However, pinpointing the exact target of the association, and identifying the phenotype it mediates, is a major challenge in the interpretation and translation of GWAS.
Overall design Transcriptome, open chromatin, and chromatin interaction profiling using RNA-seq, ATAC-seq and H3K27ac-mediated HiChIP of six immortalized mammary epithelial cell lines representing breast cells with either a luminal progenitor signature (K5+/K19+, K5+/K19-), a mesenchymal signature (B80-T17, mesHMLE) or a more epithelial like signature (B80-T5, HMLE)
Contributor(s) Beesley J
Citation(s) 36991492
Submission date Dec 01, 2022
Last update date Jun 08, 2023
Contact name Jonathan Beesley
Organization name QIMR Berghofer
Street address 300 Herston Rd Herston
City Brisbane
State/province QLD
ZIP/Postal code 4006
Country Australia
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (12)
GSM6774896 B80T17 replicate 1
GSM6774897 B80T17 replicate 2
GSM6774898 B80T5 replicate 1
This SubSeries is part of SuperSeries:
GSE219168 CRISPR screens identify gene targets at breast cancer risk loci
BioProject PRJNA907298

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

Supplementary file Size Download File type/resource
GSE219166_RAW.tar 25.6 Mb (http)(custom) TAR (of RESULTS)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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