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Series GSE79544 Query DataSets for GSE79544
Status Public on Apr 16, 2018
Title Idiopathic pulmonary fibrosis bronchoalveolar lavage cells RNA-seq indicates macrophage expression of pro-inflammatory M1/M2 activation concomitant with radical species metabolism inhibition
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Current concepts of idiopathic pulmonary fibrosis (IPF) are that microscopic injury drives alveolar epithelial cell dysregulated activation and epithelial mesenchymal transition, ensuing fibrocyte recruitment, fibroblast proliferation and ECM deposition. With the background that IPF is also characterized by chronic accumulation of activated alveolar macrophages (aMAC) in the lower respiratory tract, we assessed IPFaMAC gene expression to identify patterns of activation, by RNA-seq using Illumina platform. To this we evaluated a population of 7 normal smoking controls and 16 IPF smoking patients. All IPFs had abnormal lung function and bronchoalveolar lavage (BAL) showing >80% macrophage counts and augmented spontaneous O2 radical release. RNA was extracted from whole BAL cells. Reads were mapped onto the UCSC mRNA database (GRCh37/hg19 version), and transcripts were aggregated by gene symbol, obtaining a final 19,723 unique protein-coding gene ID list, used for further analysis.
Overall design RNA-seq transcriptomics of idiopathic pulmonary fibrosis (IPF) patients vs controls: RNA samples were extracted from macrophages obtained from bronchoalveolar lavage (BAL)
Contributor(s) Lee J, Arisi I, Puxeddu E, Mramba LK, Amicosante M, Swaisgood CM, Pallante M, Brantly ML, Saltini C
Citation(s) 29649237
Submission date Mar 23, 2016
Last update date Jul 25, 2021
Contact name Ivan Arisi
Phone +39-06-49255230
Organization name European Brain Research Institute
Department Bioinformatics Facility
Street address viale Regina Elena 295
City Roma
ZIP/Postal code 00161
Country Italy
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (23)
GSM2097611 CS1 BAL_Control
GSM2097612 CS2 BAL_Control
GSM2097613 CS4 BAL_Control
BioProject PRJNA316136
SRA SRP072242

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Supplementary file Size Download File type/resource
GSE79544_RAW.tar 9.2 Mb (http)(custom) TAR (of TXT)
GSE79544_processed_data_matrix_counts.txt.gz 789.5 Kb (ftp)(http) TXT
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Processed data are available on Series record

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