|
| Status |
Public on Nov 02, 2016 |
| Title |
EpOC from UC patient [154S] |
| Sample type |
RNA |
| |
|
| Source name |
EpOC from biopsy sample of UC patient
|
| Organism |
Homo sapiens |
| Characteristics |
case_id: 154
case_phenotype: ulcerative colitis (UC) patient
organoid_culture: EpOC
tissue: sigmoid colon
endoscopic_mayo_score: 1
uc_evolution_time (years): 8
age (years): 41
|
| Growth protocol |
Crypts from descending/sigmoid colon samples were isolated by EDTA treatment. Crypt units were embedded in Matrigel, expanded for 3-4 days in "stem medium" and dissociated. Single epithelial cells were replated in fresh "stem medium" according to a 1:3 dilution. At day 5 of in vitro expansion, total RNA was isolated from the EpOCs. Part of the EpOCs was induced to differentiate (d-EpOCs) by the addition of fresh "differentiation medium". Total RNA was isolated from d-EpOCs 5 days after differentiation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol+RNA Cleanup protocol by RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol
|
| Scan protocol |
Standard Affymetrix protocol using a Gene chip scanner 3000
|
| Description |
Gene expression data of EpOC; in vitro organoid culture derived from biopsy sample of UC patient.
|
| Data processing |
The data were analyzed with Bioconductor tools in R (version 3.1.0; http://www.r-project.org) using GC-RMA as normalization method. Next we employ a probe-filtering step, excluding those probes that showed a lower coefficient of variation or which were non-informative (not annotated).
|
| |
|
| Submission date |
Dec 11, 2015 |
| Last update date |
Nov 02, 2016 |
| 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 |
GPL20650 |
| Series (1) |
| GSE75916 |
Expression data of epithelial organoid cultures generated from intestinal mucosa of non-IBD controls and patients with ulcerative colitis |
|
