|
| Status |
Public on Oct 01, 2019 |
| Title |
Colon fibroblasts, Villincre-ERT2-ZsGreen-IhhWT-ApcKO, B4 gp38 |
| Sample type |
RNA |
| |
|
| Source name |
Sorted colon fibroblasts Epcam-CD45-CD31-gp38+
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Colon
cell type: Sorted colon fibroblasts Epcam-CD45-CD31-gp38+
genotype: Villincre-ERT2-ZsGreen-IhhWT-ApcKO
|
| Treatment protocol |
RNA from the colons was extracted with Agencourt RNAdvance Cell v2 kit (Beckman Coulter, Beverly, Massachusetts, USA) according to manufacturers’ protocol including DNA digestion step. RNA integrity and concentration were quantified with BioAnalyzer (Agilent Technologies).
|
| Growth protocol |
Villincre-ERT2-ZsGreen-IhhKO-ApcKO mice were used for colon isolation and flow-sorting experiments
|
| Extracted molecule |
total RNA |
| Extraction protocol |
2 ng RNA was amplified and labeled using 3’ IVT pico kit Affymetrix RNA amplification kit (Nugene) according to manufacturer’s protocol
|
| Label |
Biotin
|
| Label protocol |
The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for the for the hybridizations, washing, and staining of the chips. GeneChip Mouse Transcriptome Array 1.0 (MTA 1.0) (Affymetrix) according to the standard protocols of the Dutch Genomics Service and Support Provider (MAD, Science Park, University of Amsterdam, Netherlands)
|
| |
|
| Hybridization protocol |
The GeneChip Hybridization, Wash and Stain Kit (#900720) is used for scanning of the chips.
|
| Scan protocol |
The Affymetrix Command Console (v1.1) and Expression Console software (v1.1) are used to measure the performance of the washing, staining and scanning of the chips, and provide the data stored in DTT format and Cell Intensity File (*.cel) for each GeneChip processed.
|
| Data processing |
Robust Multichip Average (RMA) normalization.
|
| |
|
| Submission date |
Jul 18, 2019 |
| Last update date |
Oct 02, 2019 |
| Contact name |
Barbara Florien Westendorp |
| E-mail(s) |
[email protected]
|
| Organization name |
Academic Medical Center
|
| Department |
Tytgat Institute for Liver and Intestinal Research
|
| Lab |
Gijs van den Brink
|
| Street address |
Meibergdreef 69-71
|
| City |
Amsterdam |
| State/province |
Noord-Holland |
| ZIP/Postal code |
1105 BK |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL20775 |
| Series (1) |
| GSE134469 |
The function of the Hedgehog signaling pathway in colonic adenomagenesis |
|
