|
| Status |
Public on Jul 05, 2012 |
| Title |
ALK/MYCN 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ALK+/-, MYCN+/- tumor cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: neuroblastoma tumor
genotype: ALK+/-, MYCN+/- transgenic
genetic background: C57BL/6 x 129X1/SvJ
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from tumours using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
Samples were labeled and processed using the Agilent Low Input Quick Amp two colour Cy3 (sample) and Cy5 (mouse reference) RNA labeling kit (Stratagene) according to the manufacturer's instructions.
|
| |
|
| Channel 2 |
| Source name |
Universal Mouse Reference RNA
|
| Organism |
Mus musculus |
| Characteristics |
sample type: Stratagene Universal Mouse Reference (RNA from 11 murine cell lines)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from tumours using the miRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
Samples were labeled and processed using the Agilent Low Input Quick Amp two colour Cy3 (sample) and Cy5 (mouse reference) RNA labeling kit (Stratagene) according to the manufacturer's instructions.
|
| |
|
| |
| Hybridization protocol |
standard Agilent protocol
|
| Scan protocol |
Slides were scanned on an Agilent C Scanner at 3um using the 20bit setting.
|
| Description |
Biological replicate 1 of 5. Untreated tumour from ALK^F1174L + MYCN-expressing mice.
|
| Data processing |
Resulting data were feature extracted using Agilent Feature extraction v10.7.3. Raw data were first normalized by Agilent GeneSpring 11.5.1 software using the default normalization setting and relative expression value compared to the reference control calculated for each probe (threshold raw signals to 1, percentile shift to 75, baseline to the median of all samples). The genes with flags present in at least 100% of the values in any one out of the two groups (ALK^F1174L/MYCN and MYCN) were filtered.
|
| |
|
| Submission date |
Feb 06, 2012 |
| Last update date |
Jul 05, 2012 |
| Contact name |
Teeara Berry |
| Organization name |
The Institute of Cancer Research
|
| Department |
Paediatric Oncology
|
| Lab |
Neuroblastoma Drug Development Lab
|
| Street address |
15 Cotswold Road
|
| City |
Sutton |
| State/province |
Surrey |
| ZIP/Postal code |
SM2 5NG |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL10787 |
| Series (1) |
| GSE35560 |
Transcriptional profiles of transgenic ALK^F1174L/MYCN vs. MYCN tumors |
|
