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Series GSE148829 Query DataSets for GSE148829
Status Public on Apr 23, 2020
Title SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
Organisms Macaca fascicularis; Macaca mulatta; Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary There is pressing urgency to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) which causes the disease COVID-19. SARS-CoV-2 spike (S)-protein binds ACE2, and in concert with host proteases, principally TMPRSS2, promotes cellular entry. The cell subsets targeted by SARS-CoV-2 in host tissues, and the factors that regulate ACE2 expression, remain unknown. Here, we leverage human, non-human primate, and mouse single-cell RNA-sequencing (scRNA-seq) datasets across health and disease to uncover putative targets of SARS-CoV-2 amongst tissue-resident cell subsets. We identify ACE2 and TMPRSS2 co-expressing cells within lung type II pneumocytes, ileal absorptive enterocytes, and nasal goblet secretory cells. Strikingly, we discover that ACE2 is a human interferon-stimulated gene (ISG) in vitro using airway epithelial cells, and extend our findings to in vivo viral infections. Our data suggest that SARS-CoV-2 could exploit species-specific interferon-driven upregulation of ACE2, a tissue-protective mediator during lung injury, to enhance infection.
 
Overall design Samples from 8 datasets are included: single-cell RNA-Seq studies: 2 human adult donors of inferior turbinate scrapings with two replicates each. Four mouse donors of nasal epithelial cells, two stimulated with IFNA and two controls with two replicates from each animal. 5 non-human primate SHIV and healthy lung donors. 3 non-human primate SHIV and healthy Ileum donors. 13 human ileal small intestine donors. 10 mTB-infected non-human primates with 4 samples of granulomas from each and one sample of uninvolved lung lobe from each. 8 human lung tissue donors with mTB infection, mTB infection and HIV, or no mTB infection. Bulk RNA-seq samples: Two human donors stimulated with three replicates of each stimulation with IFNA, IFNG, IL17A, or IL4, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples. One mouse donor of cells from the trachea with three replicates of each stimulation with IFNA, IFNB, or IFNG, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples. One human cell line stimulated with three replicates of each stimulation with IFNA, IFNG, IL17A, or IL4, each at increasing doses (0, 0.1 ,0.5, 1, 2, 5, 10 ng/mL) and 12 replicates of unstimulated samples.
Submitter declares that the human raw data will be deposited in dbGaP due to patient privacy concerns.'
 
Contributor(s) Ziegler CG, Allon SJ, Nyquist SK, Mbano IM, Miao VN, Tzouanas CN, Cao Y, Yousif AS, Bals J, Hauser BM, Feldman J, Muus C, Wadsworth II MH, Kazer SW, Hughes TK, Doran B, Gatter GJ, Vukovic M, Taliaferro F, Mead BE, Guo Z, Sucre JM, Taylor CJ, Lin B, Waghray A, Mitsialis V, Dwyer DF, Buchheit KM, Boyce JA, Barrett NA, Laidlaw TM, Carroll SL, Colonna L, Tkachev V, Peterson CW, Yu A, Zheng HB, Gideon HP, Winchell CG, Lin PL, Bingle CD, Snapper SB, Kropski JA, Theis FJ, Schiller HB, Zaragosi L, Barbry P, Berger BA, Leslie A, Kiem H, Flynn JL, Fortune SM, Finberg RW, Kean LS, Garber M, Schmidt A, Lingwood D, Shalek AK, Ordovas-Montanes J
Citation(s) 32413319
Submission date Apr 17, 2020
Last update date Aug 11, 2021
Contact name Alex Shalek
E-mail(s) shalek@mit.edu
Organization name MIT
Department Chemistry
Lab Shalek Lab
Street address 45 Carleton Street
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platforms (6)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21120 Illumina NextSeq 500 (Macaca mulatta)
Samples (349)
GSM4487936 Human Scrapings SeqWell, Polyp13CEPISSS
GSM4487937 Human Scrapings SeqWell, Polyp14DEPISSS
GSM4487938 Mouse_Nasal_IFNA_High_M1_1
Relations
BioProject PRJNA627454
SRA SRP257932

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
GSE148829_BEAS_Basal_Pops_TPM.txt.gz 8.9 Mb (ftp)(http) TXT
GSE148829_Human1_Basal_Pops_TPM.txt.gz 8.0 Mb (ftp)(http) TXT
GSE148829_Human2_Basal_Pops_TPM.txt.gz 8.0 Mb (ftp)(http) TXT
GSE148829_Human_Ileum_absorptiveAndCryptentero_dge.csv.gz 8.6 Mb (ftp)(http) CSV
GSE148829_Human_lung_epithelial_cell_raw_counts.txt.gz 1.5 Mb (ftp)(http) TXT
GSE148829_Mouse_Basal_Pops_TPM.txt.gz 6.1 Mb (ftp)(http) TXT
GSE148829_NHP_TB_Grans_and_Lung_dge.txt.gz 7.0 Mb (ftp)(http) TXT
GSE148829_NHP_ileum_epithelial_raw_expression_counts.csv.gz 1.2 Mb (ftp)(http) CSV
GSE148829_NHP_lung_epithelial_raw_expression_counts.csv.gz 937.0 Kb (ftp)(http) CSV
GSE148829_NasalSSS_cleaned_raw_expression_counts.csv.gz 13.1 Mb (ftp)(http) CSV
GSE148829_RAW.tar 48.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Processed data are available on Series record
Processed data provided as supplementary file
Raw data are available in SRA
Raw data not provided for this record
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