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Status |
Public on May 15, 2013 |
Title |
A4-pre-prednisolon |
Sample type |
SRA |
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Source name |
airway smooth muscle
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Organism |
Homo sapiens |
Characteristics |
subject: A4 treatment: pre-prednisolon tissue: airway smooth muscle layer from airway wall health status: Atopic asthma
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
454 GS FLX Titanium |
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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 the prednisolon and placebo study group was carried out with the R package DESeq. RNA-Seq reads were assumed to follow a negative binomial distribution. With 12 subjects in total, 4 biopsy specimens per subject, and a significance level of 0.0001, we expected to find 68 true and 2 false significant genes. This resulted in a false discovery rate of approximately 3%. 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
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Submission date |
Sep 19, 2012 |
Last update date |
May 15, 2019 |
Contact name |
Ching Yong Yick |
E-mail(s) |
c.y.yick@amc.uva.nl
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Phone |
+31-20-5661660
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Organization name |
Academic Medical Center
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Department |
Respiratory Medicine
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Street address |
Meibergdreef 9
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City |
Amsterdam |
ZIP/Postal code |
1105AZ |
Country |
Netherlands |
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Platform ID |
GPL14603 |
Series (1) |
GSE40996 |
Steroid-induced changes in gene expression of airway smooth muscle in patients with asthma |
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Relations |
SRA |
SRX188689 |
BioSample |
SAMN01179437 |
Supplementary file |
Size |
Download |
File type/resource |
GSM1006508_A4pre_pred_GeneStatus.csv.gz |
31.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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