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Series GSE110777 Query DataSets for GSE110777
Status Public on Dec 05, 2018
Title DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease [sarcexp]
Organism Homo sapiens
Experiment type Expression profiling by array
Summary The goal of this study was to investigate and correlate differential methylation and expression in cells from the target organ in non-infectious granulomatous lung diseases, specifically sarcoidosis and chronic beryllium disease (CBD). To that end, cells were collected from patients via bronchoalveolar lavage (BAL), and extracted nucleic acids were hybridized to genome-wide arrays.
We conclude that there are many genes that are both differentially methylated and expressed in the BAL fluid of patients with granulomatous lung disease. We identified 2,726 differentially methylated CpGs mapping to 1,944 unique genes when comparing CBD patients to beryllium-sensitized (BeS) individuals without disease. 69% of these genes were also differentially expressed in CBD. Sarcoidosis patients exhibited directional consistency at many loci, but genome-wide significance was not achieved, likely due to heterogeneity in the patient population.
 
Overall design This cohort of 15 remitting and 9 progressive sarcoidosis patients, as defined in part by Scadding scale, were analyzed to detect epigenetic and transcriptomic differences within subsets of the heterogeneous sarcoidosis population. DNA and RNA were extracted from BAL fluid and analyzed on microarrays to define differential methylation and transcription genome-wide.
 
Contributor(s) Yang IV, Konigsberg IR, MacPhail K, Li L, Davidson EJ, Mroz PM, Hamzeh N, Gillespie M, Silveira LJ, Fingerlin TE, Maier LA
Citation(s) 30141971
Submission date Feb 18, 2018
Last update date Mar 06, 2019
Contact name Ivana Yang
E-mail(s) ivana.yang@ucdenver.edu
Organization name University of Colorado - Anschutz Medical Campus
Street address 12700 E 19th Ave
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
 
Platforms (1)
GPL21185 Agilent-072363 SurePrint G3 Human GE v3 8x60K Microarray 039494 [Probe Name Version]
Samples (24)
GSM3016488 Remitting sarcoidosis sample 1 [sarcexp]
GSM3016489 Remitting sarcoidosis sample 2 [sarcexp]
GSM3016490 Remitting sarcoidosis sample 3 [sarcexp]
This SubSeries is part of SuperSeries:
GSE110780 DNA Methylation Changes in Lung Immune Cells are Associated with Granulomatous Lung Disease
Relations
BioProject PRJNA434524

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE110777_RAW.tar 68.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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