|
| Status |
Public on Apr 06, 2016 |
| Title |
differentiated gallbladder organoid 2 |
| Sample type |
RNA |
| |
|
| Source name |
differentiated gallbladder organoid
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue/cell type: differentiated gallbladder organoid
|
| Treatment protocol |
Differentiated gallbladder organoids were obtained by culturing the organoids in media lacking R-spondin 1, noggin and nicotinamide for two weeks.
|
| Growth protocol |
Organoids were cultured in Matrigel with tissue culture media based on AdDMEM/F12 (Life Technologies) and supplemented with B27, N2 (Life Technologies) and 1.25 uM N-Acetylcysteine (Sigma-Aldrich). The following growth factors were also added: 50 ng/mL murine recombinant EGF (Life Technologies), 50 ng/mL murine recombinant FGF10 (R&D system), 10 mM nicotinamide (Sigma-Aldrich), 50 ng/mL murine recombinant HGF (Peprotech) and R-spondin 1 and noggin home-made conditioned media (prepared as in Sato et al., Nature 459: 262-265, 2009).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from liver, gallbladder or small intestine tissues, and liver, gallbladder or small intestine organoids using the RNeasy Mini RNA Extraction Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
5.5 ug of ds cDNA were fragmented and labeled using the GeneChip WT DNA terminal labeling kit.
|
| |
|
| Hybridization protocol |
Biotinylated cRNA was fragmented and hybridized to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix) following the standard protocol of the manufacturer.
|
| Scan protocol |
Standard Affymetrix.
|
| Description |
D2
|
| Data processing |
RMA Probes to Import: Interrogating Probes, Probe filtering: skip,Algorithm: RMA,Background Correction: RMA Background Correction,Normalization: Quantile Normalization,Log Probes using Base: 2,Probeset Summarization: Median Polish
|
| |
|
| Submission date |
Feb 02, 2016 |
| Last update date |
Apr 06, 2016 |
| Contact name |
Thanos Halazonetis |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Geneva
|
| Department |
IDepartment of Molecular Biology
|
| Lab |
Thanos Halazonetis
|
| Street address |
Sciences III, 30, quai Ernest-Ansermet
|
| City |
Geneva |
| State/province |
GE |
| ZIP/Postal code |
1211 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE77461 |
R-spondin 1 and noggin facilitate expansion of resident stem cells from non-damaged gallbladders. |
|
