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| Status |
Public on Sep 05, 2019 |
| Title |
Single-cell RNA-sequencing reveals profibrotic roles of distinct epithelial and mesenchymal lineages in pulmonary fibrosis |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Pulmonary fibrosis (PF) is a form of chronic lung disease characterized by progressive destruction of normal alveolar gas-exchange surfaces and accumulation of extracellular matrix (ECM). In order to comprehensively define the cell types, mechanisms and mediators driving ECM deposition and fibrotic remodeling in lungs with pulmonary fibrosis, we performed single-cell RNA-sequencing (scRNA-seq) of single-cell suspensions generated from non-fibrotic control and PF lungs. Analysis of over 114,000 cells from 20 PF and 10 control lungs identified 31 distinct cell types. We identified multiple distinct lineages directly contribute to ECM expansion, including a novel HAS1hi fibroblast subtype and a previously undescribed KRT5-/KRT17+, collagen and ECM-producing epithelial cell population that was highly enriched in PF lungs. Together these data provide high-resolution insights into the basic mechanisms of pulmonary fibrosis, and indicate a direct profibrotic role of the lung epithelium in PF pathogenesis.
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| Overall design |
We performed single-cell RNA-sequencing (scRNA-seq) of single-cell suspensions generated from non-fibrotic control and pulmonary fibrosis (PF) lungs
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| Contributor(s) |
Habermann AC, Gutierrez AJ, Bui LT, Winters NI, Calvi CL, Peter L, Chung M, Taylor CJ, Yahn SL, Jetter C, Raju L, Roberson J, Ding G, Wood L, Sucre JM, Richmond BW, Serezani AP, McDonnell WJ, Mallal SB, Bacchetta MJ, Shaver CM, Ware LB, Bremner R, Walia R, Blackwell TS, Banovich NE, Kropski JA |
| Citation(s) |
32832598 |
| Submission date |
Aug 16, 2019 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Nicholas Banovich |
| E-mail(s) |
nbanovich@tgen.org
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| Phone |
602-343-8432
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| Organization name |
Translational Genomics Research Institute
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| Department |
Integrated Cancer genomics division
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| Lab |
Banovich lab
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| Street address |
445 N. Fifth Street
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| City |
Phoenix |
| State/province |
AZ |
| ZIP/Postal code |
85004 |
| Country |
USA |
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| Platforms (3) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (34)
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| GSM4037300 |
Lung Biopsy, PF, VUILD55 |
| GSM4037301 |
Lung Biopsy, control, VUHD65 |
| GSM4037302 |
Lung Biopsy, control, VUHD66 |
| GSM4037303 |
Lung Biopsy, PF, VUILD57 |
| GSM4037304 |
Lung Biopsy, PF, VUILD58 |
| GSM4037305 |
Lung Biopsy, control, VUHD67 |
| GSM4037306 |
Lung Biopsy, control, VUHD68 |
| GSM4037307 |
Lung Biopsy, PF, VUILD59-2 |
| GSM4037308 |
Lung Biopsy, PF, VUILD59-1 |
| GSM4037309 |
Lung Biopsy, control, VUHD69 |
| GSM4037310 |
Lung Biopsy, PF, VUILD60-2 |
| GSM4037311 |
Lung Biopsy, PF, VUILD60-1 |
| GSM4037312 |
Lung Biopsy, PF, TILD001 |
| GSM4037313 |
Lung Biopsy, control, THD0001 |
| GSM4037314 |
Lung Biopsy, PF, VUILD61-2 |
| GSM4037315 |
Lung Biopsy, PF, VUILD61-1 |
| GSM4037316 |
Lung Biopsy, control, VUHD70 |
| GSM4037317 |
Lung Biopsy, PF, VUILD62-1 |
| GSM4037318 |
Lung Biopsy, PF, VUILD62-2 |
| GSM4037319 |
Lung Biopsy, PF, TILD015 |
| GSM4037320 |
Lung Biopsy, PF, VUILD63 |
| GSM4037321 |
Lung Biopsy, PF, VUILD64 |
| GSM4037322 |
Lung Biopsy, PF, VUILD65 |
| GSM4037323 |
Lung Biopsy, control, VUHD71 |
| GSM4037324 |
Lung Biopsy, control, THD0002 |
| GSM4037325 |
Lung Biopsy, control, THD0005 |
| GSM4037326 |
Lung Biopsy, PF, TILD006 |
| GSM4037327 |
Lung Biopsy, PF, TILD010 |
| GSM4037328 |
Lung Biopsy, PF, TILD030 |
| GSM4037329 |
Lung Biopsy, PF, TILD028 |
| GSM4037330 |
Lung Biopsy, PF, TILD019 |
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| Relations |
| BioProject |
PRJNA560492 |
| SRA |
SRP218543 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135893_ILD_annotated_fullsize.rds.gz |
20.9 Gb |
(ftp)(http) |
RDS |
| GSE135893_IPF_metadata.csv.gz |
3.2 Mb |
(ftp)(http) |
CSV |
| GSE135893_barcodes.tsv.gz |
914.9 Kb |
(ftp)(http) |
TSV |
| GSE135893_genes.tsv.gz |
126.6 Kb |
(ftp)(http) |
TSV |
| GSE135893_matrix.mtx.gz |
1.0 Gb |
(ftp)(http) |
MTX |
| GSE135893_readme_for_ILD_annotated_fullsize.rds.txt |
642 b |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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