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Status |
Public on Sep 04, 2021 |
Title |
Single cell atlas for mammals, reptiles and birds |
Organisms |
Anas platyrhynchos; Columba livia; Canis lupus familiaris; Felis catus; Capra aegagrus; Manis javanica; Oryctolagus cuniculus; Mesocricetus auratus; Anolis carolinensis; Cervus nippon taiouanus; Panthera tigris altaica |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
The availability of viral entry factors is a prerequisite for the cross-species transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Large-scale single-cell screening on animal cells is a powerful tool to reveal the expression patterns of viral entry genes for different hosts. But such exploration for SARS-CoV-2 remained limited. Here, we presented the broadest pan-species single-nucleus RNA sequencing study to date, covering 11 representative species in pets (cat, dog, hamster, lizard), livestock (goat, rabbit), poultry (duck, pigeon) and wildlife (pangolin, tiger, deer), from which we investigated the co-expression of ACE2 and TMPRSS2. Notably, the proportion of SARS-CoV-2 putative target cells in cat was found considerably higher than that of other species investigated in this study, highlighting the necessity to carefully evaluate the role of cats during SARS-CoV-2 circulation. Furthermore, cross-species analysis of comparative lung cell atlas in mammals, reptiles and birds revealed core developmental programs, critical connectomes and conserved regulatory circuits among evolutionarily distant species. Additionally, we developed a user-friendly and freely accessible online platform named PANDORA for researchers to fully exploit the pan-species single cell atlas. Overall, our work provides a compendium of gene expression profiles for non-model animals, which could be employed to identify potential SARS-CoV-2 target cells and narrow down putative zoonotic reservoirs. Alternatively, our resources could also be utilized to illuminate the cellular and molecular mechanisms underlying animal tissue evolution.
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Overall design |
To investigate the expression of SARS-CoV-2 receptors ACE2 and TMPRSS2 from 11 representative species in pets (cat, dog, hamster, lizard), livestock (goat, rabbit), poultry (duck, pigeon) and wildlife (pangolin, tiger, deer).
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Contributor(s) |
Chen D |
Citation(s) |
- Chen D, Sun J, Zhu J, Ding X et al. Single cell atlas for 11 non-model mammals, reptiles and birds. Nat Commun 2021 Dec 6;12(1):7083. PMID: 34873160
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BioProject |
PRJNA747757 |
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Submission date |
Sep 02, 2021 |
Last update date |
Jan 10, 2022 |
Contact name |
CNSA CNGB |
Organization name |
BGI
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Street address |
BGI
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City |
shenzhen |
ZIP/Postal code |
518083 |
Country |
China |
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Platforms (11)
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GPL27961 |
BGISEQ-500 (Canis lupus familiaris) |
GPL28238 |
BGISEQ-500 (Columba livia) |
GPL28431 |
BGISEQ-500 (Oryctolagus cuniculus) |
GPL29031 |
BGISEQ-500 (Capra aegagrus) |
GPL30578 |
BGISEQ-500 (Anas platyrhynchos) |
GPL30579 |
BGISEQ-500 (Anolis carolinensis) |
GPL30580 |
BGISEQ-500 (Cervus nippon taiouanus) |
GPL30581 |
BGISEQ-500 (Felis catus) |
GPL30582 |
BGISEQ-500 (Manis javanica) |
GPL30583 |
BGISEQ-500 (Mesocricetus auratus) |
GPL30584 |
BGISEQ-500 (Panthera tigris altaica) |
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Samples (29)
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Relations |
SRA |
SRP329017 |
Supplementary file |
Size |
Download |
File type/resource |
GSE183300_RAW.tar |
717.7 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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