|
| Status |
Public on Apr 17, 2007 |
| Title |
Microdissected area # 3 of 2182 tumor |
| Sample type |
RNA |
| |
|
| Source name |
Frozen neuroblastoma tumor
|
| Organism |
Homo sapiens |
| Characteristics |
Phenotype: Neuroblastoma (Schwannian stroma-poor) with areas of large neuroblastic round cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from whole tumors specimens was extracted by using the perfect RNA Eukaryotic Kit (Eppendorf, Hamburg, Germany). Instead , total RNA from LCM-derived material, was extracted by following the PicoPureTM RNA isolation kit manufacture’s instruction (Arcturus Engineering, Mountain View, CA).
|
| Label |
biotin
|
| Label protocol |
We applied the “small sample target labeling protocol” to amplify and to label targets from total RNA samples for GeneChip® probe array expression analysis (www.affymetrix.com).
|
| |
|
| Hybridization protocol |
In order to identify unscheduled hybridations, each sample was tested with a test chip containing eukaryotic control sequences including housekeeping genes. Then each sample was probed with the Human Genome U133A GeneChip® (Affymetrix, Inc., CA, USA). After prehybridization, both single test and standard probe arrays were hybridized with biotinylated cRNA hybridization cocktail at 45°C for 16 hours in the Affymetrix GeneChip® Hybridization Oven 640. Probe array wash and stain were performed in the Fluidics station. Each chip was stained with a streptavidin-phycoerythrin conjugate.
|
| Scan protocol |
GeneChips were scanned using the laser confocal fluorescence scanner.
|
| Description |
Gene expression data from microdissected area # 3 of 2182 tumor
|
| Data processing |
Image acquisition and image analysis were performed using the Affymetrix® Microarray Suite Software The probe level data from the Human Genome 133A GeneChip® were pre-processed using the affy software package (Gautier et al 2003). No background correction was performed, and probe level intensities were normalized using the vsn (Huber et al. 2002) normalization method.
|
| |
|
| Submission date |
Apr 16, 2007 |
| Last update date |
Apr 16, 2007 |
| Contact name |
Domenico Albino |
| E-mail(s) |
[email protected]
|
| Phone |
+39-010-5737463
|
| Organization name |
National Institute for Cancer Research (IST)
|
| Street address |
L.go R. Benzi, 10
|
| City |
genoa |
| ZIP/Postal code |
16132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE7529 |
Two distinct gene signatures identify malignant Neuroblast and Schwannian stromal cells of Neuroblastic Tumors |
|
