|
| Status |
Public on Dec 31, 2021 |
| Title |
c3b.P013_08_Tum_Apc_cr_P34_b |
| Sample type |
RNA |
| |
|
| Source name |
Apc+/1638N small intestinal adenoma cells (n=3) from mouse P34 Technical replicate of d1a
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Apc+/1638N
gender: male
strain: C57Bl/6
tissue: Small Intestine
|
| Treatment protocol |
SI crypts were isolated from wt C57BL/6 mice and cultured in a 3D culture system. For an indirect co-culture SI MFs were seeded on the insert (Transwell, 24 mm diameter insert, 0.4 µm pore size, tissue culture treated polyester membrane, Corning) that was placed in a 6-well plate. Cells were cultured overnight in a medium composed of RPMI, 10% FBS and 1% penicillin/ streptomycin. Then, SI organoids were mixed with Matrigel and seeded in the 6-well plate, below the insert. Cells were cultured for 24 h in the Basal Medium. After that, organoids were harvested for RNA isolation.
|
| Growth protocol |
Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using RNeasy mini Qiagen kit according to the manufacturer’s guidelines.
|
| Label |
biotin
|
| Label protocol |
150 ng RNA was amplified, biotin labeled and fragmented using the Ambion WT Expression kit and GeneChip WT Terminal Labeling and Controls kit.
|
| |
|
| Hybridization protocol |
60 ul (25 ng/ul) of fragemented and labeled cDNA was hybridized to Mouse Genome 2.1ST GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.
|
| Scan protocol |
Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.
|
| Data processing |
Data was normalized using the RMA algorithm as implemented in Bioconductor/R.
|
| |
|
| Submission date |
Jan 04, 2019 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Michael Quante |
| E-mail(s) |
michael.quante@tum.de
|
| Organization name |
Technische Universität München
|
| Department |
II Medizinische Klinik
|
| Street address |
Ismaninger Str 22
|
| City |
München |
| ZIP/Postal code |
81675 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17400 |
| Series (1) |
| GSE124684 |
Gene expression of mouse small intestinal 3D organoid myofibroblast-epithelium co-culture |
|
