|
| Status |
Public on Jun 01, 2016 |
| Title |
TA2 untreated 2 |
| Sample type |
RNA |
| |
|
| Source name |
TA2 untreated
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: organoid culture of tubular adenoma
organoid: TA2
treatment: control
batch: 2
|
| Treatment protocol |
Organoid cultures were treated for 5 days with A83-01 (control condition/untreated) or 5 ng/ml recombinant human TGF-β1.
|
| Growth protocol |
Organoid cultures were isolated from patient material and cultured accodring to standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the NucleoSpin RNA II kit from Macherey-Nagel.
|
| Label |
biotin
|
| Label protocol |
Labeling was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.
|
| |
|
| Hybridization protocol |
Hybridization was performed according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.
|
| Scan protocol |
Samples were scanned using the Gene Titan Affymetrix instrument according to the standard protocols of the Cologne Center for Genomics (CCG), University of Cologne, Germany.
|
| Description |
Gene expression from colon tumor organoid TA2 untreated
|
| Data processing |
Data were normalized by RMA using the Affy R package and batch effects were removed using the Combat algorithm as implemented in the sva R package
|
| |
|
| Submission date |
Mar 21, 2016 |
| Last update date |
Jun 01, 2016 |
| Contact name |
Sander Roeland van Hooff |
| Organization name |
AUMC
|
| Department |
Center for Experimental and Molecular Medicine (CEMM),
|
| Lab |
Laboratory for Experimental Oncology and Radiobiology (LEXOR)
|
| Street address |
Meibergdreef 9
|
| City |
Amsterdam |
| ZIP/Postal code |
1105 AZ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL13158 |
| Series (2) |
| GSE79461 |
TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype [organoids] |
| GSE79462 |
TGFβ signaling directs serrated adenomas to the mesenchymal colorectal cancer subtype |
|
