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Series GSE52778 Query DataSets for GSE52778
Status Public on Jan 01, 2014
Title Human Airway Smooth Muscle Transcriptome Changes in Response to Asthma Medications
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Rationale: Asthma is a chronic inflammatory airway disease. The most common medications used for its treatment are β2-agonists and glucocorticosteroids, and one of the primary tissues that these drugs target in the treatment of asthma is the airway smooth muscle. We used RNA-Seq to characterize the human airway smooth muscle (HASM) transcriptome at baseline and under three asthma treatment conditions.
Methods: The Illumina TruSeq assay was used to prepare 75bp paired-end libraries for HASM cells from four white male donors under four treatment conditions: 1) no treatment; 2) treatment with a β2-agonist (i.e. Albuterol, 1μM for 18h); 3) treatment with a glucocorticosteroid (i.e. Dexamethasone (Dex), 1μM for 18h); 4) simultaneous treatment with a β2-agonist and glucocorticoid, and the libraries were sequenced with an Illumina Hi-Seq 2000 instrument. The Tuxedo Suite Tools were used to align reads to the hg19 reference genome, assemble transcripts, and perform differential expression analysis using the protocol described in https://github.com/blancahimes/taffeta
 
Overall design mRNA profiles obtained via RNA-Seq for four primary human airway smooth muscle cell lines that were treated with dexamethasone, albuterol, dexamethasone+albuterol or were left untreated.
 
Contributor(s) Himes B, Lu Q
Citation(s) 24926665
Submission date Nov 26, 2013
Last update date Mar 20, 2019
Contact name Blanca E Himes
E-mail bhimes@pennmedicine.upenn.edu
Organization name University of Pennsylvania
Department Department of Biostatistics, Epidemiology and Informatics
Lab 402 Blockley Hall
Street address 423 Guardian Dr
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (16)
GSM1275862 N61311_untreated
GSM1275863 N61311_Dex
GSM1275864 N61311_Alb
Relations
BioProject PRJNA229998
SRA SRP033351

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
GSE52778_All_Sample_FPKM_Matrix.txt.gz 2.5 Mb (ftp)(http) TXT
GSE52778_Dex_vs_Untreated_gene_exp.diff.gz 830.1 Kb (ftp)(http) DIFF
Raw data are available in SRA
Processed data is available on Series record

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