|
| Status |
Public on Apr 13, 2021 |
| Title |
BRN2_HOM_TUM_3 |
| Sample type |
RNA |
| |
|
| Source name |
Primary tumor
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Tyr::CreErT2::BrafV600E F/+ Pten F/+ BRN2 F/F
Sex: female
rin: 8.2
category: Braf-Pten-Brn2-hom
mouseid: 19A-21-22-28 1510
|
| Growth protocol |
Newborn mice were treated dorsally with 0.4 μg/day/mouse tamoxifen from P1 to P3. Developing skin excrescences > 3 mm diameter were considered to be melanomas, and validated after growth. Mice were sacrificed and autopsied four weeks after tumor appearance or once the tumors reached 2 cm3. Only melanoma having a volume of 1cm^3 were used for the transcriptomic analysis. For mice harbouring multiple melanome, only the biggest melanomas on each mouse was harvested. Tumors were then excised, rinsed in cold PBS and snap-frozen in liquid nitrogen.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the miRneasy, Qiagen extraction kit according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
The IVT reaction was carried out in the presence of T7 RNA polymerase and a biotinylated nucleotide analog/ribonucleotide mix for cRNA amplification and biotin labelling.
|
| |
|
| Hybridization protocol |
Complementary RNA (cRNA) was synthesized using the GeneChip 3′IVT Plus reagent Kit, according to the manufacturer’s protocol. Then 11μg cRNA were hybridized to mouse MOE430 gene expression Affymetrix microarrays
|
| Scan protocol |
After washing and staining, using the Affymetrix fluidics station 450, the probe arrays were scanned using an Affymetrix GeneChip Scanner 3000.
|
| Data processing |
Data processing was done using R/Bioconductor. CEL files were read using the oligo package and normalized using the RMA - Robust Multichip Average algorithm. The highest-IQR probe for each gene was retained.
|
| |
|
| Submission date |
Dec 12, 2020 |
| Last update date |
Apr 13, 2021 |
| Contact name |
Lionel Larue |
| Phone |
+33 1 69 86 71 07
|
| Organization name |
Institut Curie
|
| Department |
UMR3347 CNRS - U1021 INSERM, Institut Curie
|
| Lab |
Normal and Pathological Development of Melanocytes
|
| Street address |
Bat 110, Centre universitaire
|
| City |
Orsay |
| ZIP/Postal code |
91405 |
| Country |
France |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE126524 |
Gene expression data from Tyr::CreErT2::BrafV600E Pten F/+ mouse tumors according to defloxing status of Brn2 [tumors] |
| GSE163086 |
Gene expression data from Tyr::CreErT2::BrafV600E Pten F/+ mouse tumors according to defloxing status of Brn2 |
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