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Sample GSM182297 Query DataSets for GSM182297
Status Public on Apr 17, 2007
Title Microdissected area # 1 of 1919 tumor
Sample type RNA
Source name Frozen neuroblastoma tumor
Organism Homo sapiens
Characteristics Phenotype: Neuroblastoma (Schwannian stroma-poor) with areas of large round neuroblastic 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 (
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 # 1of 1919 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
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

Data table header descriptions
VALUE Summary expression indexes were computed using the medianpolish method, and only perfect match probes were used (Gautier et al (2004)).

Data table
1007_s_at 7.820125324
1053_at 5.569835825
117_at 5.812771467
121_at 7.516123928
1255_g_at 5.344162911
1294_at 6.647009972
1316_at 5.814287156
1320_at 5.220270441
1405_i_at 5.829142296
1431_at 4.622237156
1438_at 6.831178285
1487_at 6.374716276
1494_f_at 6.412039513
1598_g_at 8.369645712
160020_at 7.478873236
1729_at 6.473107777
177_at 5.237015844
1773_at 5.735010905
179_at 8.053012018
1861_at 5.977930126

Total number of rows: 22283

Table truncated, full table size 497 Kbytes.

Supplementary file Size Download File type/resource
GSM182297.CEL.gz 1.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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