Table 1 Summary of single-cell RNA-sequencing studies of healthy and fibrotic human lung tissue
From: From COVID to fibrosis: lessons from single-cell analyses of the human lung
Authors | Sample breakdown | Number of cells | Technology used | Validation study | Data availability |
|---|---|---|---|---|---|
Adams et al. [20] | 32 IPF, 18 COPD, 28 healthy controls | 312,928 | 10X Genomics 3’ Chromium system | IHC, other datasets | GEO GSE136831, www.IPFcellatlas.com |
Reyfman et al. [19] | 8 donor lung biopsies, 8 lung explants: 4 IPF, 2 SSc-ILD, 1 polymyositis, 1 CHP | 76,070 | 10X Genomics 3’ v2 Chromium system | ISH, IHC | nupulmonary.org/resources, www.IPFcellatlas.com |
Habermann et al. [21] | 20 PF (12 IPF, 3 CHP, 2 NSIP, 2 sarcoidosis, 1 unclassifiable ILD), 10 healthy controls | 114,396 | 10X Genomics 3’ v2 and 5’ v1 Chromium systems | ISH | GEO GSE135893, www.IPFcellatlas.com |
Melms et al. [33] | 19 severe COVID-19, 8 healthy controls | 116,000 | 10X Genomics 3’ v3.1 Chromium system (single nuclei) | IHC, multiplexed microscopy, imaging mass cytometry | GEO GSE171524 |
Travaglini et al, [7] | 3 nonsmoker and smoker controls |  ~ 75,000 | 10X Genomics 3’ Chromium system (65,662 cells) and Smart-Seq2 (9,404 cells) | ISH, flow cytometry | https://www.synapse.org/#!Synapse:syn21041850 European Genome-Phenome Archive EGAS00001004344 |
Hasan et al. [46] | 3 moderate COVID-19, 12 severe COVID-19, 5 decreased COVID-19, 6 healthy controls (meta-analysis) | Not reported | 10X Genomics 5’ and 3’ | NA | GEO GSE1618215, GSE169471, GSE145926 (lungs) |
Schupp et al. [47] | 73 healthy controls (meta-analysis) |  ~ 15,000 vascular cells | 10X Genomics | IF, ISH, IHC | GEO GSE164829, www.lungendothelialcellatlas.com |
Delorey et al. [35] | 16 deceased COVID-19 (lung-only) | 106,792 | 10X Genomics scRNA-Seq, snRNA-seq | RNAscope, ISH | GEO GSE171668, DUOS (raw human sequencing data): duos.broadinstitute.org |
Tsukui et al. [49] | 3 IPF, 2 s SSc-ILD | 83,316 | 10X Genomics 3’ v2 | ISH, IHC | GEO GSE132771, GSE147066 |
Bahrat et al. [36] | 5 severe COVID (3 explants, 2 donor) | Not reported | 10X Genomics 3’ v3 | ISH | GSE158127 https://github.com/NUPulmonary/2020_Bharat. Single-cell RNA-sequencing data |
Morse et al. [44] | 3 healthy lungs, 3 IPF lower lobe, 3 IPF upper lobe | 47,771 | 10X Genomics 3’ v1 or v2 | IHC, IF | GEO GSE128033, IPFcellatlas.com |