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| Status |
Public on May 10, 2024 |
| Title |
Single-cell genomics & regulatory networks for 388 human brains |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet, little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multi-omics datasets into a resource comprising >2.8M nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550K cell-type-specific regulatory elements and >1.4M single-cell expression-quantitative-trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.
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| Overall design |
Single nuclei were isolated from human postmortem dlPFC from normal control group and sequenced for transcription profile (snRNA-seq) and chromatin accessibility (snATAC-seq)
Please note that RT00389N is a duplicate of RT00374N, and therefore shares the same metadata for both sample IDs.
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| Contributor(s) |
Clarke D, Dursun C, Emani P, Gupta C, Jensen M, Lee CY, Liu J, Lou S, Meng R, Warrell J, Xu S, Chen Y, Chu Z, Galeev T, Hwang A, Ni P, Zhou X, Bakken T, Bicks L, Chatterjee T, Cheng L, Cheng Y, Dai Y, Duan Z, Flaherty M, Gaynor S, Grundman J, Hawken N, Henry E, Huang A, Jin T, Jorstad N, Kawaguchi R, Liu J, Liu J, Liu S, Ma S, Margolis M, Mazariegos S, Moore J, Moran J, Nguyen E, Phalke N, Pratt H, Quintero D, Rajagopalan A, Riesenmy T, Shedd N, Shi M, Spector M, Terwilliger R, Travaglini K, Wamsley B, Wang G, Xiao S, Yang A, Zheng S, Lein E, Sestan N, Weng Z, White K, Won H, Girgenti M, Zhang J, Wang D, Geschwind D, Gerstein M |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Mar 20, 2024 |
| Last update date |
May 10, 2024 |
| Contact name |
Jing Zhang |
| Organization name |
University of California, Irvine
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| Street address |
University of California, Irvine
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| City |
Irvine |
| State/province |
CA |
| ZIP/Postal code |
92697 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA1089984 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE261983_ATAC_peakset.bed.gz |
4.7 Mb |
(ftp)(http) |
BED |
| GSE261983_RAW.tar |
5.3 Gb |
(http)(custom) |
TAR (of MTX, TXT) |
| GSE261983_RNA_gene_list.txt.gz |
126.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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