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Series GSE135893 Query DataSets for GSE135893
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
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.
Overall design We performed single-cell RNA-sequencing (scRNA-seq) of single-cell suspensions generated from non-fibrotic control and pulmonary fibrosis (PF) lungs
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
Phone 602-343-8432
Organization name Translational Genomics Research Institute
Department Integrated Cancer genomics division
Lab Banovich lab
Street address 445 N. Fifth Street
City Phoenix
State/province AZ
ZIP/Postal code 85004
Country USA
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (34)
GSM4037297 Lung Biopsy, PF, VUILD48
GSM4037298 Lung Biopsy, PF, VUILD54
GSM4037299 Lung Biopsy, PF, VUILD53
BioProject PRJNA560492
SRA SRP218543

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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
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Raw data are available in SRA
Processed data are available on Series record

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