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Status |
Public on Apr 17, 2007 |
Title |
Microdissected area # 1 of 1761 tumor |
Sample type |
RNA |
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Source name |
Frozen borderline ganglioneuroma maturing tumor
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Organism |
Homo sapiens |
Characteristics |
Phenotype: Borderline ganglioneuroma maturing with areas of schwannian stromal cells
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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).
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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.
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Scan protocol |
GeneChips were scanned using the laser confocal fluorescence scanner.
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Description |
Gene expression data from microdissected area # 1 of 1761 tumor
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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.
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Submission date |
Apr 16, 2007 |
Last update date |
Apr 16, 2007 |
Contact name |
Domenico Albino |
E-mail(s) |
domenico.albino@istge.it
|
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 |
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