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Series GSE89013 Query DataSets for GSE89013
Status Public on Dec 19, 2016
Title Identification of Breast Cancer Associated Variants That Modulate Transcription Factor Binding
Organism Homo sapiens
Experiment type Other
Summary GWAS have discovered thousands of genomic loci that are associated with disease risk and quantitative traits, but most of the variants responsible for risk remain uncharacterized. The vast majority of GWAS-identified loci contain non-coding SNPs and defining molecular mechanism of risk is challenging. Many non-coding causal SNPs are hypothesized to alter Transcription Factor (TF) binding sites as the mechanism by which they affect organismal phenotypes. We employed an integrative genomics approach to identify candidate TF binding motifs that confer breast cancer-specific phenotypes identified by GWAS. We performed de novo motif analysis of regulatory elements, analyzed evolutionary conservation of identified motifs, and assayed TF footprinting data to identify sequence elements that recruit TFs and maintain chromatin landscape in breast cancer-relevant tissue and cell lines. Regulatory elements for MCF10A were mapped with ATAC-seq.We identified top candidate causal SNPs that are predicted to alter TF binding, within breast cancer-relevant regulatory regions, and in strong linkage disequilibrium with the GWAS SNPs. This integrative analysis pipeline is a general framework to identify candidate causal variants within regulatory regions and TF binding sites that confer phenotypic variation and disease risk.
Overall design Map the hypersensitve regions in breast cancer specific cell lines. Identfy TF motifs that underlie the overexpressed regions. Using GWAS ipute causal SNPs that could disrupt TF binding site. Five biological replicate libraries were prepared and sequenced paired end (2x75).
Contributor(s) Walavalkar N, Guertin M
Citation(s) 28957321
Submission date Oct 20, 2016
Last update date May 15, 2019
Contact name Michael Guertin
Organization name University Of Virginia
Street address 1340 Jefferson Park Ave
City Charlottesville
State/province Virginia
ZIP/Postal code 22908
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (5)
GSM2357376 MCF10a_rep1
GSM2357377 MCF10a_rep2
GSM2357378 MCF10a_rep3
BioProject PRJNA349763
SRA SRP091892

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Supplementary file Size Download File type/resource
GSE89013_MCF10a_merged.bedGraph.gz 189.3 Mb (ftp)(http) BEDGRAPH
GSE89013_MCF10a_merged.bigWig 190.7 Mb (ftp)(http) BIGWIG 2.0 Mb (ftp)(http) BED
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