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Series GSE164013 Query DataSets for GSE164013
Status Public on Apr 11, 2021
Title A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2 [gene expression levels]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary The SARS-CoV-2 pandemic has caused over 1 million deaths globally, mostly due to acute lung injury and acute respiratory distress syndrome, or direct complications resulting in multiple-organ failures. Little is known about the host tissue immune and cellular responses associated with COVID-19 infection, symptoms, and lethality. To address this, we collected tissues from 11 organs during the clinical autopsy of 17 individuals who succumbed to COVID-19, resulting in a tissue bank of approximately 420 specimens. We generated comprehensive cellular maps capturing COVID-19 biology related to patients’ demise through single-cell and single-nucleus RNA-Seq of lung, kidney, liver and heart tissues, and further contextualized our findings through spatial RNA profiling of distinct lung regions. We developed a computational framework that incorporates removal of ambient RNA and automated cell type annotation to facilitate comparison with other healthy and diseased tissue atlases. In the lung, we uncovered significantly altered transcriptional programs within the epithelial, immune and stromal compartments and cell intrinsic changes in multiple cell types relative to lung tissue from healthy controls. We observed evidence of alveolar type 2 (AT2) differentiation replacing depleted alveolar type 1 (AT1) lung epithelial cells, as previously seen in fibrosis, and a concomitant increase in myofibroblasts reflective of defective tissue repair. Viral reads were enriched in lung mononuclear phagocytic cells and endothelial cells, and these cells expressed distinct viral RNA host response transcriptional programs. We corroborated the compositional and transcriptional changes in lung tissue through spatial analysis of RNA profiles in situ and distinguished unique tissue host responses between regions with and without viral RNA, and in COVID-19 donor tissues relative to healthy lung. Finally, we analyzed genetic regions implicated in COVID-19 GWAS with transcriptomic data to implicate specific cell types and genes associated with disease severity. Overall, our COVID-19 cell atlas is a foundational dataset to better understand the biological impact of SARS-CoV-2 infection across the human body and empowers the identification of new therapeutic interventions and prevention strategies.
 
Overall design This dataset contains gene expression levels from ROIs from autopsy FFPE lung tissues from a cohort of 5 patients with positive SARS-CoV-2 nasopharyngeal swab on admission. A total of 80 ROIs were collected and segmented to 80 AOIs.

WTA = Nanostring GeoMx Digital Spatial Profiling (DSP) Whole Transcriptome Atlas (WTA) Panel
 
Contributor(s) Pita-Juarez YH, Vlachos IS
Citation(s) 33915569
Submission date Dec 29, 2020
Last update date Jul 12, 2021
Contact name Yered Hammurabi Pita-Juarez
E-mail(s) yhpitaju@bidmc.harvard.edu
Organization name Beth Israel Deaconess Medical Center
Department Pathology
Lab Vlachos Lab
Street address 330 Brookline Ave
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (80)
GSM4994854 D13_Parenchyma_ROI1_Geometric
GSM4994855 D13_Parenchyma_ROI2_Geometric
GSM4994856 D13_Parenchyma_ROI3_Geometric
This SubSeries is part of SuperSeries:
GSE163530 A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
Relations
BioProject PRJNA688513
SRA SRP299689

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
GSE164013_GeoMx_WTA_COVID19_v1.0.pkc.txt.gz 2.1 Mb (ftp)(http) TXT
GSE164013_Q3Norm_TargetCountMatrix.tsv.gz 5.1 Mb (ftp)(http) TSV
GSE164013_RAW.tar 5.1 Mb (http)(custom) TAR (of DCC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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