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| Status |
Public on Aug 15, 2014 |
| Title |
Atopic asthma airway smooth muscle A6 |
| Sample type |
SRA |
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| Source name |
airway smooth muscle
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| Organism |
Homo sapiens |
| Characteristics |
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 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
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| 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
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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) |
| GSE38003 |
Transcriptomic Analysis of Airway Smooth Muscle by Next-Generation Sequencing (RNA-Seq): Asthma versus Healthy Controls |
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| Relations |
| SRA |
SRX148365 |
| BioSample |
SAMN00996424 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM931716_A6_GeneStatus.csv.gz |
33.0 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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