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| Status |
Public on Feb 09, 2017 |
| Title |
Population STARR-seq in preadipocytes pre/post differentiation |
| Organism |
Homo sapiens |
| Experiment type |
Other
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| Summary |
Transversions (Tv's) are more likely to alter the amino acid sequence of proteins than transitions (Ts's), and local deviations in the Ts:Tv ratio are indicative of evolutionary selection on genes. Whether the two different types of mutations have different effects in non-protein-coding sequences remains unknown. Here, we provide multiple lines of evidence demonstrating that Tv’s have larger impacts on regulatory DNA including analyses of transcription factor (TF) binding motifs, allele-specific TF binding, and genome-wide Tv density within accessible chromatin. Using massively parallel population-scale reporter assays, we also provide empirical evidence that Tv's have larger effects than Ts's on the activity of human gene regulatory elements. Understanding the features of functional non-coding variation will be valuable for revealing the genetic underpinnings of complex traits and diseases.
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| Overall design |
STARR-seq libraries were generated from captured open chromatin regions at 3q25 in 760 individuals and transfected into HepG2 cells.
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| Contributor(s) |
Guo C, McDowell IC, Nodzenski M, Scholtens DM, Lowe WL, Reddy TE |
| Citation(s) |
28525990 |
| Submission date |
Feb 09, 2016 |
| Last update date |
Sep 25, 2019 |
| Contact name |
Timothy E Reddy |
| E-mail(s) |
tim.reddy@duke.edu
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| Organization name |
Duke University
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| Lab |
Tim Reddy
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| Street address |
101 Science Dr. RM 2383
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| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
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| Platforms (1) |
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| Samples (4)
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| GSM2058394 |
Population STARR-seq Input Plasmid Library |
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| Relations |
| BioProject |
PRJNA311336 |
| SRA |
SRP069829 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE77743_Haplotype_effects.txt.gz |
18.8 Kb |
(ftp)(http) |
TXT |
| GSE77743_Haplotypes.fasta.gz |
50.3 Kb |
(ftp)(http) |
FASTA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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