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Series GSE202963 Query DataSets for GSE202963
Status Public on Dec 07, 2022
Title A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection [bulk RNA-seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary COVID-19 is a systemic disease involving multiple organs. Human pluripotent stem cells (hPSCs) derived organoids/cells provide insight into cellular tropism and host response, yet the molecular mechanisms regulating SARS-CoV-2 infection remain poorly defined. Here, we systematically examined changes in transcript profiles caused by SARS-CoV-2 infection at different MOIs for airway organoids (AWOs), alveolar organoids (ALOs) and cardiomyocytes (CMs), and identified several genes, including CIART, that are generally implicated in controlling SARS-CoV-2 infection. AWOs, ALOs, and CMs derived from isogenic CIART-/- hPSCs were significantly resistant to SARS-CoV-2 infection, independent of viral entry. Single-cell RNA-seq further validated the decreased levels of SARS-CoV-2 infection in multi-ciliated cells of AWOs. CUT&RUN, ATAC-seq and RNA-seq analyses found that CIART controls SARS-CoV-2 infection at least in part through regulating NR4A1, a gene also identified from the multi-organoid analysis. Finally, transcriptional profiling and pharmacological inhibition revealed that the Retinoid X Receptor (RXR) pathway regulates SARS-CoV-2 infection downstream of CIART/NR4A1. The multi-organoid platform provides potential therapeutic targets for protection against COVID-19 across organ systems.
 
Overall design RNA-seq was used to systematically profile transcriptional changes of hPSC-derived airway organoids, alveolar organoids and cardiomyocytes caused by SARS-CoV-2 infection.
 
Contributor(s) Tang X, Xue D, Zhang T, Nilsson-Payant B, Chen S
Citation(s) 36918693
Submission date May 13, 2022
Last update date Jul 14, 2023
Contact name Shuibing Chen
E-mail(s) shuibing.chen@gmail.com
Phone 2127465431
Organization name Weill Cornell Medical College
Department Surgery
Street address A 827B, 1300 York Ave
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (71)
GSM6139273 Airway 48h Mock_1 [bulk RNA-seq]
GSM6139274 Airway 48h Mock_2 [bulk RNA-seq]
GSM6139275 Airway 48h Mock_3 [bulk RNA-seq]
This SubSeries is part of SuperSeries:
GSE202967 A Multi-Organoid Platform Identifies CIART as a Key Factor for SARS-CoV-2 Infection.
Relations
BioProject PRJNA837900

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
GSE202963_counts.ALO.48h.txt.gz 486.6 Kb (ftp)(http) TXT
GSE202963_counts.ALO.downsample.txt.gz 555.6 Kb (ftp)(http) TXT
GSE202963_counts.AWO.48h.txt.gz 569.8 Kb (ftp)(http) TXT
GSE202963_counts.AWO.downsample.txt.gz 528.0 Kb (ftp)(http) TXT
GSE202963_counts.CM.48h.txt.gz 579.6 Kb (ftp)(http) TXT
GSE202963_counts.CM.downsample.txt.gz 443.9 Kb (ftp)(http) TXT
GSE202963_rld.ALO.48h.txt.gz 3.3 Mb (ftp)(http) TXT
GSE202963_rld.ALO.txt.gz 3.4 Mb (ftp)(http) TXT
GSE202963_rld.AWO.48h.txt.gz 3.8 Mb (ftp)(http) TXT
GSE202963_rld.AWO.txt.gz 3.3 Mb (ftp)(http) TXT
GSE202963_rld.CM.48h.txt.gz 3.7 Mb (ftp)(http) TXT
GSE202963_rld.CM.txt.gz 3.2 Mb (ftp)(http) TXT
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