|
| Status |
Public on Jan 07, 2011 |
| Title |
27051402_setdb1_3 |
| Sample type |
RNA |
| |
|
| Source name |
MiniCoopR-SETDB1_3 melanoma
|
| Organism |
Danio rerio |
| Characteristics |
genotype: p53-M214k; mitf -/-; mitf:BRAF-V600E
tissue: melanoma
transposon vector: MiniCoopR-SETDB1
|
| Growth protocol |
Zebrafish of the indicated genotype were mated, and embryos were injected with either MiniCoopR-GFP or MiniCoopR-SETDB1 transposon vectors. Transgenic zebrafish with melanocytes were raised to adulthood. Zebrafish with dorsal melanomas were isolated, and melanomas were allowed to grow for 3 weeks from the date of onset.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invitrogen, USA).
|
| Label |
Cy3
|
| Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| |
|
| Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
|
| Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
|
| Description |
This sample is of MiniCoopR-SETDB1 melanoma. It is one of four biological replicates used in the experiment.
|
| Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
|
| |
|
| Submission date |
May 05, 2010 |
| Last update date |
Jan 07, 2011 |
| Contact name |
Yariv Houvras |
| Organization name |
Childrens Hospital Boston
|
| Street address |
1 Blackfan Circle
|
| City |
Karp 7 |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL10392 |
| Series (2) |
| GSE21505 |
Expression analysis of melanoma harvested from GFP versus SETDB1 transgenic zebrafish (Danio rerio) |
| GSE26372 |
Expression analysis of melanoma harvested after GFP or SETDB1 expression |
|
