|
| Status |
Public on Nov 26, 2019 |
| Title |
Massively Parallel Reporter Assay of human-specific substitutions in neurodevelopmental enhancers |
| Organisms |
Pan troglodytes; Homo sapiens |
| Experiment type |
Other
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
We performed a Massively Parallel Reporter Assay (MPRA) to screen >30,000 human-specific substitutions in ChIP-seq-identified Human Gain Enhancers (HGEs) and Human Accelerated Regions (HARs), highly conserved non-coding regions that show accelerated sequence evolution in humans. After comparing human and chimpanzee reference alleles, we used a second MPRA to deconvolute individual substitutions within differentially active enhancers from substitutions in the same fragment and from other variants (human segregating variants or chimpanzee-specific variants) to isolate their specific effects on enhancer activity.
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| |
|
| Overall design |
This submission contains data for two MPRA experiments. MPRA1 contains data for an inert library, a competent library, and four experimental replicates. MPRA2 contains data for an inert library and two experimental replicates. This submission also contains ATAC-seq data for hNSCs (three replicates).
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| |
|
| Contributor(s) |
Uebbing S, Gockley J, Noonan JP |
| Citation(s) |
33372131 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 GM094780 |
Identifying enhancers with human-specific developmental functions |
YALE UNIVERSITY |
James P Noonan |
|
| |
| Submission date |
Nov 25, 2019 |
| Last update date |
Feb 01, 2021 |
| Contact name |
James Patrick Noonan |
| E-mail(s) |
james.noonan@yale.edu
|
| Organization name |
Yale University
|
| Department |
Genetics
|
| Street address |
333 Cedar Street
|
| City |
New Haven |
| State/province |
CT |
| ZIP/Postal code |
06520 |
| Country |
USA |
| |
|
| Platforms (4)
|
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL27802 |
Illumina HiSeq 2500 (Homo sapiens; Pan troglodytes) |
| GPL27803 |
Illumina HiSeq 4000 (Homo sapiens; Pan troglodytes) |
| GPL27804 |
Illumina NovaSeq 6000 (Homo sapiens; Pan troglodytes) |
|
| Samples (18)
|
| GSM4191883 |
Experimental plasmid DNA replicate 2 ("22") for MPRA1 |
| GSM4191884 |
Experimental plasmid DNA replicate 3 ("13") for MPRA1 |
| GSM4191885 |
Experimental plasmid DNA replicate 4 ("23") for MPRA1 |
| GSM4191886 |
Experimental cDNA replicate 1 ("12") for MPRA1 |
| GSM4191887 |
Experimental cDNA replicate 2 ("22") for MPRA1 |
| GSM4191888 |
Experimental cDNA replicate 3 ("13") for MPRA1 |
| GSM4191889 |
Experimental cDNA replicate 4 ("23") for MPRA1 |
| GSM4191890 |
Inert library for MPRA2 |
| GSM4191891 |
Experimental plasmid DNA replicate 1 for MPRA2 |
| GSM4191892 |
Experimental plasmid DNA replicate 2 for MPRA2 |
| GSM4191893 |
Experimental cDNA replicate 1 for MPRA2 |
| GSM4191894 |
Experimental cDNA replicate 2 for MPRA2 |
| GSM4191895 |
ATAC-seq replicate 1 ("P5-1") |
| GSM4191896 |
ATAC-seq replicate 2 ("P5-2") |
| GSM4191897 |
ATAC-seq replicate 3 ("P15-1") |
|
| Relations |
| BioProject |
PRJNA591611 |
| SRA |
SRP233214 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE140983_COUNTS_ANNOTATED.txt.gz |
386.5 Mb |
(ftp)(http) |
TXT |
| GSE140983_MPRAcounts.tsv.gz |
109.6 Mb |
(ftp)(http) |
TSV |
| GSE140983_P15-1_peaks.bigbed |
4.0 Mb |
(ftp)(http) |
BIGBED |
| GSE140983_P15-1_treat_pileup.bw |
108.0 Mb |
(ftp)(http) |
BW |
| GSE140983_P5-1_peaks.bigbed |
3.3 Mb |
(ftp)(http) |
BIGBED |
| GSE140983_P5-1_treat_pileup.bw |
124.0 Mb |
(ftp)(http) |
BW |
| GSE140983_P5-2_peaks.bigbed |
3.4 Mb |
(ftp)(http) |
BIGBED |
| GSE140983_P5-2_treat_pileup.bw |
108.3 Mb |
(ftp)(http) |
BW |
| GSE140983_hNSC_50_peaks.bigbed |
5.6 Mb |
(ftp)(http) |
BIGBED |
| GSE140983_hNSC_50_treat_pileup.bw |
297.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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