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Series GSE196235 Query DataSets for GSE196235
Status Public on Mar 09, 2022
Title Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary We present a joint single-cell atlas of gene expression and chromatin accessibility of the adult human retina. We integrate this atlas with a HiChIP enhancer connectome, expression quantitative trait loci (eQTL) data, and base-resolution deep learning models to predict noncoding variants with causal roles in eye disease.
 
Overall design Single-cell RNA-seq, single-cell ATAC-seq, and HiChIP
Please note that the processed data for the ATAC-seq and RNA-seq samples were generated from all replicates and are linked to the corresponding rep1 sample records.
 
Contributor(s) Wang SK, Chang HY
Citation(s) 36277849
Submission date Feb 07, 2022
Last update date Oct 31, 2022
Contact name Sean K Wang
E-mail(s) seankw@stanford.edu
Organization name Stanford University
Street address 1291 Welch Rd
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (3)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL21697 NextSeq 550 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (18)
GSM5866071 Human retina H3K27ac HiChIP rep2 [HiChIP_LGS1OD]
GSM5866072 Human retina H3K27ac HiChIP rep1 [HiChIP_LVG1OD]
GSM5866073 Human retina scATAC rep3 [scATAC_LGS1OD]
Relations
BioProject PRJNA803994

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
GSE196235_RAW.tar 10.0 Gb (http)(custom) TAR (of BEDPE, HIC, MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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