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Series GSE171524 Query DataSets for GSE171524
Status Public on Apr 29, 2021
Title Columbia University/NYP COVID-19 Lung Atlas
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary We profiled 116,314 cells using snRNA-seq of 20 frozen lungs obtained from 19 COVID-19 decedents and seven control patients with short postmortem interval (PMI) autopsies. The COVID-19 cohort comprises seven female and 12 male decedents, including 13 patients of Hispanic ethnicity, with an age range from 58 to >89 years who had acquired SARS-CoV-2 infection and succumbed to the disease. The average time from symptom onset to death was 27.5 days (range, 4–63 days). After rapid autopsy with a median PMI of 4 hours (range 2–9 hours) collected tissues were either flash-frozen or frozen following OCT (optimal cutting temperature) embedment and subjected to snRNA-seq using a droplet-based platform (10x Genomics). All included patients had underlying hypertensive disorder and frequently one or more additional co-morbidities associated with increased risk for severe COVID-19.
Overall design Single-nuclei RNA sequencing of 116,314 cells from 20 frozen lungs obtained from 19 COVID-19 decedents and seven control patients.

Raw read files to be uploaded to DUOS ( due to patient privacy concerns.
Web link
Contributor(s) Izar B, Melms JC, Biermann J
Citation(s) 33915568
Submission date Apr 05, 2021
Last update date Sep 20, 2021
Contact name Jana Biermann
Organization name Columbia University
Street address 622 West 168th St
City New York
State/province NY
ZIP/Postal code 10032
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (27)
GSM5226574 C51ctr snRNA-seq
GSM5226575 C52ctr snRNA-seq
GSM5226576 C53ctr snRNA-seq
BioProject PRJNA719842

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
GSE171524_RAW.tar 161.9 Mb (http)(custom) TAR (of CSV)
GSE171524_lung_metaData.txt.gz 1.2 Mb (ftp)(http) TXT
GSE171524_processed_data.csv.gz 1.6 Gb (ftp)(http) CSV
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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