Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
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Updated June 16, 2022We isolated single cells (using either liberase or collagenase A dissociation) from subcutaneous adipose tissue collected from abdominoplasty surgery, and healthy liver tissue adjacent to tumor from liver resection and ran 10X v2 3' scRNA Seq.
Malte D LueckenInstitute of Computational Biology, Helmholtz Zentrum Münchenmalte.luecken@helmholtz-muenchen.de
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. (Official HCA Publication)
Christoph Muus1
Malte D Luecken2
Gökcen Eraslan1
Lisa Sikkema2
Avinash Waghray3
Graham Heimberg1
Yoshihiko Kobayashi4
Eeshit Dhaval Vaishnav1
Ayshwarya Subramanian1
Christopher Smillie1
Karthik A Jagadeesh1
Elizabeth Thu Duong5
Evgenij Fiskin1
Elena Torlai Triglia1
Meshal Ansari6
Peiwen Cai7
Brian Lin8
Justin Buchanan9
Sijia Chen10
Jian Shu11
Adam L Haber1
Hattie Chung1
Daniel T Montoro1
Taylor Adams12
Hananeh Aliee2
Samuel J Allon11
Zaneta Andrusivova13
Ilias Angelidis6
Orr Ashenberg1
Kevin Bassler14
Christophe Bécavin15
Inbal Benhar1
Joseph Bergenstråhle13
Ludvig Bergenstråhle13
Liam Bolt16
Emelie Braun17
Linh T Bui18
Steven Callori19
Mark Chaffin20
Evgeny Chichelnitskiy21
Joshua Chiou22
Thomas M Conlon6
Michael S Cuoco1
Anna SE Cuomo23
Marie Deprez15
Grant Duclos24
Denise Fine25
David S Fischer2
Shila Ghazanfar26
Astrid Gillich27
Bruno Giotti28
Joshua Gould1
Minzhe Guo29
Austin J Gutierrez18
Arun C Habermann30
Tyler Harvey1
Peng He16
Xiaomeng Hou31
Lijuan Hu17
Yan Hu32
Alok Jaiswal1
Lu Ji33
Peiyong Jiang33
Theodoros S Kapellos34
Christin S Kuo35
Ludvig Larsson13
Michael A Leney-Greene1
Kyungtae Lim36
Monika Litviňuková37
Leif S Ludwig1
Soeren Lukassen38
Wendy Luo1
Henrike Maatz39
Elo Madissoon40
Lira Mamanova16
Kasidet Manakongtreecheep11
Sylvie Leroy41
Christoph H Mayr42
Ian M Mbano43
Alexi M McAdams44
Ahmad N Nabhan27
Sarah K Nyquist45
Lolita Penland27
Olivier B Poirion31
Sergio Poli12
CanCan Qi46
Rachel Queen47
Daniel Reichart48
Ivan Rosas12
Jonas C Schupp49
Conor V Shea50
Xingyi Shi50
Rahul Sinha51
Rene V Sit27
Kamil Slowikowski45
Michal Slyper1
Neal P Smith52
Alex Sountoulidis53
Maximilian Strunz54
Travis B Sullivan55
Dawei Sun36
Carlos Talavera-López56
Peng Tan1
Jessica Tantivit11
Kyle J Travaglini57
Nathan R Tucker20
Katherine A Vernon11
Marc H Wadsworth11
Julia Waldman1
Xiuting Wang7
Ke Xu50
Wenjun Yan58
William Zhao7
Carly GK Ziegler11
1Klarman Cell Observatory, Broad Institute of MIT and Harvard
2Institute of Computational Biology, Helmholtz Zentrum München
3Center for Regenerative Medicine, Massachusetts General Hospital
4Department of Cell Biology, Duke University Medical School
5Division of Respiratory Medicine, Department of Pediatrics, University of California
6Comprehensive Pneumology Center (CPC)/Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL)
7Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai
8Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care Unit, Massachusetts General Hospital
9Center for Epigenomics, University of California San Diego School of Medicine
10Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Harvard Medical School
11Broad Institute of MIT and Harvard
12Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine
13SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology
14Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn
15Université Côte d'Azur, CNRS, IPMC
16Wellcome Sanger Institute
17Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute
18Translational Genomics Research Institute
19Department of Medicine, Boston University School of Medicine
20Precision Cardiology Laboratory, The Broad Institute
21Institute of Transplant Immunology, Hannover Medical School, MHH
22Biomedical Sciences Graduate Program, University of California, San Diego
23European Molecular Biology Laboratory, European Bioinformatics Institute
24Boston University School of Medicine
25Boston University Medical Center, Boston, MA, USA.
26Cancer Research UK Cambridge Institute, University of Cambridge
27Department of Biochemistry and Wall Center for Pulmonary Vascular Disease
28Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai
29Divisions of Pulmonary Biology; Perinatal Institute, Cincinnati Children's Hospital Medical Center
30Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center
31Center for Epigenomics, University of California-San Diego School of Medicine
32Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado
33Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories
34Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn
35Division of Pulmonary Medicine, Department of Pediatrics, Stanford University
36Gurdon Institute, University of Cambridge
37Cellular Genetics Programme, Wellcome Sanger Institute
38Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health
39Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)
40European Molecular Biology Laboratory-European Bioinformatics Institute
41Pulmonology Department, Université Côte d'Azur, CHU Nice
42Helmholtz Zentrum München, Institute of Lung Biology and Disease, Group Systems Medicine of Chronic Lung Disease, Member of the German Center for Lung Research (DZL)
43Africa Health Research Institute
44Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear
45Broad Institute of MIT and Harvard, Cambridge
46Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen
47Biosciences Institute, Faculty of Medical Sciences, Newcastle University, International Centre for Life
48Department of Genetics, Harvard Medical School
49Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA.
50Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine
51Institute for Stem Cell Biology and Regenerative Medicine, Stanford Medicine
52Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital
53Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University
54Comprehensive Pneumology Center (CPC) and Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL)
55Lahey Hospital & Medical Center, Burlington
56Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus
57Department of Biochemistry and Wall Center for Pulmonary Vascular Disease, Stanford, CA, USA.
58Center for Brain Science, Harvard University
Ami Day
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Atlas
None
Analysis Portals
UCSC Cell BrowserProject Label
CrossTissueSARS-CoV-2StudySpecies
Homo sapiens
Sample Type
specimens
Anatomical Entity
2 anatomical entities
Organ Part
Unspecified
Selected Cell Types
Unspecified
Disease Status (Specimen)
normal
Disease Status (Donor)
2 disease statuses
Development Stage
human adult stage
Library Construction Method
10x 3' v2
Nucleic Acid Source
single cell
Paired End
falseAnalysis Protocol
analysis_protocol_cell_types, analysis_protocol_quantificationFile Format
2 file formats
Cell Count Estimate
24.3kDonor Count
7csv.gz2 file(s)h5ad.gz2 file(s)