|
| Status |
Public on Sep 11, 2017 |
| Title |
Active CD_0405S |
| Sample type |
RNA |
| |
|
| 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: anti-TNF
endoscopic_mayo_score: n.a.
cdeis: 5.4
partial cdeis: 21
ibd_evolution_time (years): 12
age (years): 21
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)
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol
|
| Scan protocol |
Standard Affymetrix protocol using a Gene chip scanner 3000
|
| Description |
Gene expression data from blood; peripheral whole blood sample from CD patient collected at the time of endoscopic evaluation
|
| 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).
|
| |
|
| 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 |
|
