|
| Status |
Public on Jun 12, 2019 |
| Title |
243_STEM_3h_5mM |
| Sample type |
RNA |
| |
|
| Source name |
EpOCs from Ctrl (243), 3h incubation, 5 mM butyrate stimulation
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: 243
differentiated_organoid: Epithelial organoid cultures (EpOCs)
stimulus_time: 3h
stimulus_conc: 5mM
|
| Treatment protocol |
At day 5 of in vitro expansion, EpOCs were stimulated with 0.5 mM and 5 mM butyrate during 1h, 3h, 6h or 24h and total RNA was isolated. d-EpOCs were stimulated with 0.5 mM and 5 mM butyrate during 1h, 3h, 6h or 24h and total RNA was isolated.
|
| 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 to generate EpOCs. Part of the EpOCs was induced to differentiate (d-EpOCs) by the addition of fresh differentiation medium.
|
| 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 |
3h 5 mM
243_6
|
| 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.
|
| |
|
| Submission date |
Dec 10, 2018 |
| Last update date |
Jun 12, 2019 |
| 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) |
| GSE123553 |
Expression data of butyrate stimulated epithelial organoid cultures generated from intestinal mucosa |
|
