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| Status |
Public on Nov 01, 2020 |
| Title |
A human cell atlas of fetal gene expression |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The gene expression program underlying the specification of human cell types is of fundamental interest. We generated human cell atlases of gene expression and chromatin accessibility in fetal tissues. For gene expression, we applied three-level combinatorial indexing to >110 samples representing 15 organs, profiling ~4 million single cells. We leveraged the literature and other atlases to identify and annotate hundreds of cell types and subtypes, both within and across tissues. Our analyses focus on organ-specific specializations of broadly distributed cell types (e.g. blood, endothelial, epithelial), sites of fetal erythropoiesis (which surprisingly included the adrenal gland) and integration with mouse developmental atlases (e.g. conserved specification of blood cells). These data comprise a rich resource for the exploration of in vivo human gene expression in diverse tissues and cell types.
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| Overall design |
single cell RNA-seq profiling of human fetal tissues
***RNA-Seq raw data is to be made available through dbGaP (controlled access) due to privacy concerns:
https://www.ncbi.nlm.nih.gov/gap/?term=phs002003.v1.p1
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| Contributor(s) |
Cao J, O'Day DR, Pliner HA, Kingsley P, Deng M, Daza RM, Zager MA, Kimberly A, Blecher R, Zhang F, O'Day DR, Spielmann M, Palis J, Doherty D, Steemers FJ, Glass IA, Trapnell C, Shendure J |
| Citation(s) |
33184181 |
| Submission date |
Aug 24, 2020 |
| Last update date |
Aug 26, 2021 |
| Contact name |
Junyue Cao |
| E-mail(s) |
cao1025@uw.edu
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| Organization name |
University of Washington
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| Department |
Department of Genome Sciences
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| Lab |
Shendure lab
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| Street address |
Foege Building S-210, 3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (121)
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| Relations |
| BioProject |
PRJNA659041 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156793_S1_metadata_cells.txt.gz |
333.0 Mb |
(ftp)(http) |
TXT |
| GSE156793_S2_Metadata_genes.txt.gz |
564.7 Kb |
(ftp)(http) |
TXT |
| GSE156793_S3_gene_count.loom.gz |
12.1 Gb |
(ftp)(http) |
LOOM |
| GSE156793_S4_gene_expression_tissue.txt.gz |
5.5 Mb |
(ftp)(http) |
TXT |
| GSE156793_S5_gene_fraction_tissue.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| GSE156793_S6_gene_expression_celltype.txt.gz |
33.1 Mb |
(ftp)(http) |
TXT |
| GSE156793_S7_gene_fraction_celltype.txt.gz |
25.5 Mb |
(ftp)(http) |
TXT |
| GSE156793_S8_DE_gene_cells.csv.gz |
13.3 Mb |
(ftp)(http) |
CSV |
| Raw data not provided for this record |
| Processed data are available on Series record |
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