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Sample GSM931711 Query DataSets for GSM931711
Status Public on Aug 15, 2014
Title Atopic asthma airway smooth muscle A1
Sample type SRA
 
Source name airway smooth muscle
Organism Homo sapiens
Characteristics tissue: airway smooth muscle layer from airway wall
health status: Atopic asthma
Extracted molecule total RNA
Extraction protocol 4 endobronchial biopsies per subject were collected during a bronchoscopy. Airway smooth muscle was collected from the biopsies by laser capture microdissection and total RNA isolated with TRIzol. cDNA was prepared using the Ovation RNA-Seq System (NuGEN). cDNA libraries of >350bp were constructed using SPRIworks Fragment Library System II (Beckman Coulter) with the addition of GS FLX Titanium Rapid Library multiplex identifier (MID) adaptors (Roche). Emulsion-based clonal amplification was performed using the GS FLX Titanium emPCR Kit (Lib-L; Roche). RNA-Seq was performed using the GS FLX+ instrument (454/Roche).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model 454 GS FLX Titanium
 
Data processing The general quality of the sequencing run was checked using the GS Run Browser version 2.6 (Roche).
Sequence reads were mapped against the human genome (hg19; UCSC) using the GS Reference Mapper version 2.6 (Roche).
Comparison of the numbers of reads per gene between asthma and healthy controls was based on the negative binomial distribution and carried out with the R package DESeq including correction for multiple testing.
With 24 subjects in total, 4 biopsy specimens per subject, and a significance level of 0.0001, we expected to find 310 true and 2 false significant genes. This resulted in a false discovery rate of approximately 1%.
Genome_build: hg19
Supplementary_files_format_and_content: Comma-separated files contain mapped genes and the following information: number of unique matching reads, percent of all unique matches, percent of all reads
 
Submission date May 16, 2012
Last update date May 15, 2019
Contact name Ching Yong Yick
E-mail(s) c.y.yick@amc.uva.nl
Phone +31-20-5661660
Organization name Academic Medical Center
Department Respiratory Medicine
Street address Meibergdreef 9
City Amsterdam
ZIP/Postal code 1105AZ
Country Netherlands
 
Platform ID GPL14603
Series (1)
GSE38003 Transcriptomic Analysis of Airway Smooth Muscle by Next-Generation Sequencing (RNA-Seq): Asthma versus Healthy Controls
Relations
Reanalyzed by GSE81474
SRA SRX148360
BioSample SAMN00996419

Supplementary file Size Download File type/resource
GSM931711_A1_GeneStatus.csv.gz 27.5 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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