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Status |
Public on Sep 11, 2017 |
Title |
Active CD_0144S |
Sample type |
RNA |
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|
Source name |
Human peripheral whole blood from endoscopically active CD patient
|
Organism |
Homo sapiens |
Characteristics |
subject status: Crohn's disease (CD) patient case_phenotype: Crohn endoscopic_activity: Active disease_extension: ileocolonic treatment: 5-asa endoscopic_mayo_score: n.a. cdeis: 14 partial cdeis: 25 ibd_evolution_time (years): 9 age (years): 30 gender: Female tissue: peripheral whole blood microarray_batch: 1
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the PAXgene Blood RNA Kit (Qiagen, Spain) in a QIAcube instrument (Qiagene, Spain) following the manufacturer's instructions. Additional DNase Treatment & Removal (Ambion, Life Technologies, USA) was used to safely eliminate DNA contamination from RNA samples.
|
Label |
biotin
|
Label protocol |
The derived cDNA from whole blood was produced by Ovation® PicoSL WTA System V2 (NuGEN, USA)
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Hybridization protocol |
Standard Affymetrix protocol
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Scan protocol |
Standard Affymetrix protocol using a Gene chip scanner 3000
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Description |
Gene expression data from blood; peripheral whole blood sample from CD patient collected at the time of endoscopic evaluation
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Data processing |
The data was analyzed with Bioconductor tools in R (version 3.1.0; http://www.r-project.org) using RMA as normalization method. Probes were summarized using the revised entrez-based probe annotation of Dai (package hug133plus2hsentrezgcdf, version 18.0.1). Then, data was adjusted for batch effects using the ComBat method. Next we employ a probe-filtering step, excluding those probes that showed a lower coefficient of variation, low intensity levels in all observations (<5) or which were non-informative (not annotated).
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|
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Submission date |
Feb 08, 2017 |
Last update date |
Sep 11, 2017 |
Contact name |
Azucena Salas |
E-mail(s) |
asalas1@recerca.clinic.cat
|
Organization name |
IDIBAPS
|
Department |
Gastroenterology
|
Street address |
Rosselló, 149-153
|
City |
Barcelona |
ZIP/Postal code |
08036 |
Country |
Spain |
|
|
Platform ID |
GPL19109 |
Series (1) |
GSE94648 |
Expression data from peripheral whole blood of non-IBD controls, CD and UC patients |
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