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Series GSE86618 Query DataSets for GSE86618
Status Public on Dec 08, 2016
Title Single Cell RNA-Sequencing Identifies Diverse Roles of Epithelial Cells in Idiopathic Pulmonary Fibrosis
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease causing alveolar remodeling, inflammation, and fibrosis. We utilized single cell RNA-sequencing (scRNA-Seq) to identify epithelial cell types and associated biological processes involved in the pathogenesis of IPF. Transcriptomic analysis of epithelial cells from normal human lung defined gene expression patterns associated with highly differentiated alveolar type 2 (AT2) cells, indicated by enrichment of RNAs critical for surfactant homeostasis. In contrast, scRNA-seq of IPF cells identified three distinct subsets of epithelial cell types with characteristics of conducting airway basal and goblet cells and, an additional atypical "transitional" cell that contribute to pathological processes in IPF. Individual IPF cells frequently co-expressed alveolar AT1, AT2, and conducting airway selective markers, demonstrating "indeterminate" states of differentiation not seen in normal lung development. Pathway analysis predicted aberrant activation of canonical signaling via TGF-ß, HIPPO/YAP, P53, and AKT-PI3 Kinase. Immunofluorescence confocal microscopy identified the disruption of alveolar structure and loss of the normal proximal-peripheral differentiation of pulmonary epithelial cells. Single cell transcriptomic analyses of respiratory epithelial cells identified loss of normal epithelial cell identities and unique contributions of epithelial cells to the pathogenesis of IPF. Present scRNA-seq transcriptomic analysis of normal and IPF respiratory epithelial cells provides a rich data source to further explore lung health and disease.
Overall design Examination of expression profiling at single-cell level between IPF and Control.
Contributor(s) Xu Y, Mizuno T, Tang J, Funari VA, Stripp BR, Whitsett JA
Citation(s) 27942595
Submission date Sep 09, 2016
Last update date May 15, 2019
Contact name Jie Tang
Organization name Cedars Sinai Medical Center
Street address 8700 Beverly Blvd
City Los Angeles
ZIP/Postal code 90048
Country USA
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (540)
GSM2306940 01-H12.CC019
GSM2306941 01-N701-S517-A1.CC002
GSM2306942 01-N701-S517-B5.IPF009
BioProject PRJNA342415
SRA SRP087726

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Supplementary file Size Download File type/resource
GSE86618_34816genes-540cells-tpm.txt.gz 27.3 Mb (ftp)(http) TXT
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Raw data are available in SRA

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