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| Status |
Public on Apr 30, 2022 |
| Title |
Dissecting genetic components associated with eye disease using integrative genomic analysis [ATAC-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
GWAS studies have revealed thousands of variants strongly associated with AMD, yet connecting these variants to their cognate genes has not been explored. In this study we fine-mapped AMD risk loci and examined long-range cis chromatin interactions at essential genes of RPE function and disease-associated variants in iPSC-induced retinal pigmented epithelium (RPE) and primary RPE.
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| Overall design |
ATAC-seq from iPSCs (2 replicates), iPSC-induced RPE (3 replicates) and primary RPE (3 replicates)
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| Contributor(s) |
Jamieson K, Shen Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Apr 27, 2022 |
| Last update date |
May 02, 2022 |
| Contact name |
Kirsty Jamieson |
| E-mail(s) |
kirstyjamieson@gmail.com
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| Organization name |
University of California
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| Street address |
400 Parnassus Ave
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| City |
San Francisco |
| ZIP/Postal code |
94143 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (8)
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| GSM6069383 |
ATAC-seq, iPSC-induced RPE, biol rep2 |
| GSM6069384 |
ATAC-seq, iPSC-induced RPE, biol rep3 |
| GSM6069385 |
ATAC-seq, primary RPE, biol rep1 |
| GSM6069386 |
ATAC-seq, primary RPE, biol rep2 |
| GSM6069387 |
ATAC-seq, primary RPE, biol rep3 |
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| This SubSeries is part of SuperSeries: |
| GSE201681 |
Dissecting genetic components associated with eye disease using integrative genomic analysis |
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| Relations |
| BioProject |
PRJNA832665 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE201677_ATAC-seq_iPSC-induced_RPE.bed.gz |
657.9 Kb |
(ftp)(http) |
BED |
| GSE201677_ATAC-seq_iPSCs.bed.gz |
252.7 Kb |
(ftp)(http) |
BED |
| GSE201677_ATAC-seq_primary_RPE.bed.gz |
360.9 Kb |
(ftp)(http) |
BED |
| GSE201677_RAW.tar |
4.2 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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