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Series GSE135188 Query DataSets for GSE135188
Status Public on Dec 31, 2019
Title Intermittent exposure to whole cigarette smoke alters the differentiation of primary small airway epithelial cells in the air-liquid interface culture
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Cigarette smoke (CS) is the leading cause to develop COPD. Therefore, we investigated the pathologic effects of whole CS on the differentiation of primary small airway epithelial cells (SAEC), from three healthy donors and three COPD patients, cultured under ALI (air-liquid interface) conditions. The analysis of the epithelial physiology demonstrated that CS impaired barrier formation and reduced cilia beat activity. Although, COPD-derived ALI cultures preserved some features known from COPD patients, the CS-induced effects were similarly pronounced in ALI cultures from patients compared to healthy controls. A RNA sequencing analysis revealed the deregulation for marker genes for basal cells and secretory cells upon CS exposure. The comparison between gene signatures obtained from our in vitro model (CS vs. air) with a published data set from human epithelial brushes (smoker vs. non-smoker) reveals a high degree of similarity between the deregulated genes and pathways. ALI culture has been generated utilising cells obtained from 3 COPD and 3 healthy subjects. Subsequently cultures have been treated with CS and air respectively for 33 days. Gene expression profiles were generated using next generation sequencing.
Overall design ALI culture mRNA profiles of COPD and healthy control subjects. Cells from 3 COPD and 3 healthy control donors have been split into 6 ALI cultures, each, resulting in overall 36 culture wells. Half of the wells per donor have been treated with CS and the other half with air. Expression data were generated using Illumina HiSeq3000.
Contributor(s) Gindele J, Quast K, Schymeinsky J
Citation(s) 32277131
Submission date Jul 31, 2019
Last update date Apr 20, 2020
Contact name Karsten Quast
Organization name Boehringer Ingelheim Pharma GmbH & Co. KG
Department Computational Biology
Street address Birkendorfer Str. 65
City Biberach
ZIP/Postal code 88397
Country Germany
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (36)
GSM3993154 A_CS_1
GSM3993155 A_CS_2
GSM3993156 A_CS_3
BioProject PRJNA557685
SRA SRP216947

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Supplementary file Size Download File type/resource
GSE135188_uniqueRPKM.txt.gz 2.8 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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