|
| Status |
Public on Sep 01, 2020 |
| Title |
Patient 3 CSC-Media |
| Sample type |
RNA |
| |
|
| Source name |
colon cancer organoids patient 3
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon cancer organoids
patient: 3
|
| Treatment protocol |
For FGFR-inhibition experiments, FGF2 and EGF were omitted from the medium and 10 µM SU-5402 (Sigma) was added. SU-5402 powder was solved in DMSO (30 mM) according to the manufacturer’s protocol and was diluted 1:3,000 for a working concentration. The same DMSO dilution was equally added to control experiments.
|
| Growth protocol |
Primary patient-derived cells were cultured as organoids in growth-factor-reduced Matrigel (Corning, phenol red-free) droplets (5,000 cells per 50 µl Matrigel droplet). Matrigel droplets were covered with 500 µl Cancer Stem Cell Medium (CSCM) consisting of Advanced DMEM/F12, 10 mM Hepes, 1% GlutaMAX, B-27 media supplement without retinoic acid, N-2 media supplement, 2 µg/ml Heparin, 1 mM N-Acetylcystein, 50 ng/ml human EGF, 50 ng/ml human FGF2, 10 µM Y-27632 and antibiotics/antimycotics. Medium was changed every other day. After 48 h of culturing, Y-27632 was omitted from the media and antibiotics/ antimycotics treatment was reduced to 100 U/ml Penicillin and 100 µg/ml Streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufacturer's protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Standard Affymetrix hybridization protocol.
|
| Scan protocol |
Standard Affymetrix scanning protocol for PrimeView Human Gene Expression Array.
|
| Description |
Replicate 1
|
| Data processing |
The data were normalised using RMA normalisation from R/Bioconductor.
|
| |
|
| Submission date |
Aug 22, 2018 |
| Last update date |
Sep 02, 2020 |
| Contact name |
Wasco Wruck |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitätsklinikum Düsseldorf
|
| Street address |
Moorenstr. 5
|
| City |
Düsseldorf |
| ZIP/Postal code |
40225 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16043 |
| Series (1) |
| GSE118949 |
FGF Signaling in the Self-Renewal of Colon Cancer Organoids |
|
