HCA Data Explorer

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets.

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Updated June 6, 2023

The authors generated single-cell atlases of 23 lung, 16 kidney, 15 liver and 18 heart COVID-19 autopsy donor tissue samples, and spatial atlases of 14 lung donors.

Aviv RegevBroad Institute of MIT and Harvardaviv.regev.sc@gmail.com
Ori Rozenblatt-RosenBroad Institute of MIT and Harvardorit.r.rosen@gmail.com
Alexandra-Chloe VillaniBroad Institute of MIT and Harvardavillani@mgh.harvard.edu
Alex K ShalekBroad Institute of MIT and Harvardshalek@mit.edu
Aviv Regev1
Ori Rozenblatt-Rosen1
Alexandra-Chloe Villani1
Alex K Shalek1
Bo Li1
Caroline BM Porter1
Orr Ashenberg1
Isaac H Solomon2
Ioannis S Vlachos1
James R Stone3
Samouil L Farhi1
Mehrtash Babadi1
Dejan Juric4
Z Gordon Jiang4
Donald E Ingber4
Robert Rogers5
Richard Novak4
Pardis C Sabeti1
Deborah Hung1
Timothy L Tickle1
Gyongyi Szabo1
Stefan Riedel4
Purushothama Rao Tata6
Jayarai Rajagopal7
Alkes L Price8
Winston Hide4
Nir Hacohen1
Rajat M Gupta1
Lisa Cosimi2
Daniel R Zollinger9
Shuting Zhang1
Sarah Warren9
Avinash Waghray10
Ellen Todres1
Alexander Sturm1
Michelle Siciliano2
Erroll H Rueckert9
Melissa Rudy1
Marty Ross9
Jason Reeves9
Jacob Plaisted2
Christopher J Pinto4
Jenna Pfiffner-Borges1
Carmel Pe’er1
Deepti Pant5
Liuliu Pan9
Robert Padera2
Mari Niemi11
Christoph Muus1
Eric M Miller9
Daniel E McLoughlin7
Cristin McCabe1
Hui Ma1
Michael Leney-Greene1
Judit Jane-Valbuena1
Tyler Hether9
Jonathan Hecht4
Tyler Harvey1
John Gryzb2
Joshua Gould1
Steven Gazal12
Robin Fropf9
Donna M Fitzgerald7
Adam Essene5
Jesse M Engreitz1
Phylicia Dorceus1
Prajan Divakar9
Jonathan Chen1
Olga R Brook5
Joseph Beechem9
Deepak S Atri1
Liat Amir-Zilberstein1
Liping Wang13
Shamsudheen K Vellarikkal1
Victoria M Tran1
Malika Sud1
Katherine J Siddle1
Linus TY Tsai1
Sebastian Niezen4
Siddarth S Raju1
Yury V Popov4
Pourya Naderi4
Erica Normandin1
Igor Katsyv13
James Gomez1
Johannes C Melms13
Andrea Ganna11
Nick Barkas1
Zohar Bloom-Ackerman1
Jana Biermann13
Devan Phillips1
Yered H Pita-Juarez1
Michal Slyper1
Pritha Sen1
Kushal K Dey14
Karthik A Jagadeesh1
Toni M Delorey1
Carly G Ziegler1
Graham Heimberg1
Rachelly Normand1
Yiming Yang1
Asa Segerstolpe1
Domenic Abbondanza1
Stephen J Fleming1
Ayshwarya Subramanian1
Daniel T Montoro1
1Broad Institute of MIT and Harvard
2Brigham and Women's Hospital
3Massachusetts General Hospital, Harvard Medical School,
4Harvard Medical School
5Beth Israel Deaconess Medical Center
6Duke University School of Medicine
7Massachusetts General Hospital
8Harvard University
9NanoString Technologies Inc
10Harvard Stem Cell Institute
11Institute for Molecular Medicine Finland
12University of Southern California
13Columbia University Irving Medical Center
14Harvard T. H. Chan School of Public Health, Harvard University
Ami Day

To reference this project, please use the following link:

https://explore.data.humancellatlas.org/projects/61515820-5bb8-45d0-8d12-f0850222ecf0

Supplementary links are provided by contributors and represent items such as additional data which can’t be hosted here; code that was used to analyze this data; or tools and visualizations associated with this specific dataset.

1.https://duos.broadinstitute.org/dataset_statistics/1792.https://duos.broadinstitute.org/dataset_statistics/1803.https://duos.broadinstitute.org/dataset_statistics/181
INSDC Project Accessions:
SRP297414, SRP299689
GEO Series Accessions:
GSE171668, GSE162911, GSE164013
INSDC Study Accessions:
PRJNA720539, PRJNA683801, PRJNA688513

Downloaded and exported data is governed by the HCA Data Release Policy and licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). For more information please see our Data Use Agreement.

Atlas

None

Analysis Portals

None

Project Label

GSE171668_SingleCellAndSpatialAtlasCovid

Species

Homo sapiens

Sample Type

specimens

Anatomical Entity

8 anatomical entities

Organ Part

13 organ parts

Selected Cell Types

Unspecified

Disease Status (Specimen)

5 disease statuses

Disease Status (Donor)

5 disease statuses

Development Stage

human adult stage

Library Construction Method

4 library construction methods

Nucleic Acid Source

3 nucleic acid sources

Paired End

false, true

Analysis Protocol

analysis_protocol_bulk, analysis_protocol_sc, analysis_protocol_spatial_dsp

File Format

10 file formats

Cell Count Estimate

106.8k

Donor Count

32
csv.gz4 file(s)fastq.gz2,428 file(s)jpg2 file(s)pkc.gz3 file(s)png3,857 file(s)tar3 file(s)tiff86 file(s)tsv.gz1 file(s)txt.gz2 file(s)xlsx3 file(s)