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Series GSE165765 Query DataSets for GSE165765
Status Public on Jan 30, 2021
Title A Dinucleotide-barcode reporter system and application in dissecting the causal rule of regulatory risk SNPs
Organisms Homo sapiens; synthetic construct
Experiment type Genome variation profiling by high throughput sequencing
Summary We adapted the DiR barcode-based parallel reporter assay systems strategy to systematically identify the SNPs that affect gene expression by modulating activities of regulatory elements. Among 293 SNPs linked with GWAS-identified prostate cancer-risk SNPs, we found 32, 9, and 11 regulatory SNPs in 22Rv1, PC-3, and LNCaP cells. Further mechanism study indicates that one SNP regulates gene expression in prostate cancer malignancy. The DiR system has great potential to advance the functional study of risk SNPs that have associations with polygenic diseases. Our findings hold great promise in benefiting prostate cancer patients with prognostic prediction.
 
Overall design Blank DiR-seq bias analysis in LNCaP cell lines (3 replicates), Input plasmid library 10lib before transfection (3 replicates). Blank DiR-seq report analysis in LNCaP and MCF7 cell lines (3 replicates, respectively), Input plasmid library before transfection (3 replicates). SNP DiR-seq report analysis in 22Rv1, PC-3 and LNCaP cell lines (3 replicates, respectively), Input plasmid library before transfection (2 replicates).
 
Contributor(s) Ren N, Li B, Liu Q
Citation(s) 34445492
Submission date Jan 29, 2021
Last update date Aug 31, 2021
Contact name Qilai Huang
E-mail(s) qlhuang@sdu.edu.cn
Phone 18651633196
Organization name Shandong University
Street address Binhai road 72#
City QingDao
ZIP/Postal code 266237
Country China
 
Platforms (3)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL26697 HiSeq X Ten (synthetic construct)
GPL29673 HiSeq X Ten (Homo sapiens; synthetic construct)
Samples (11)
GSM5049682 Sample D701
GSM5049683 Sample D702
GSM5049684 Sample D703
Relations
BioProject PRJNA697854
SRA SRP303802

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
GSE165765_SNP_barcode_id.txt.gz 2.5 Kb (ftp)(http) TXT
GSE165765_raw_counts.tar.gz 19.5 Mb (ftp)(http) TAR
GSE165765_sample-to-library_relationships.txt.gz 1.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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