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Sample GSM182299 Query DataSets for GSM182299
Status Public on Apr 17, 2007
Title Whole ganglioneuroblastoma intermixed tumor_1999
Sample type RNA
 
Source name frozen ganglioneuroblastoma intermixed tumor
Organism Homo sapiens
Characteristics Phenotype: Ganglioneuroblastoma, intermixed (Schwannian stroma-rich)
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 whole 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) 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

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

Data table
ID_REF VALUE
1007_s_at 10.16743715
1053_at 7.907814856
117_at 8.385659666
121_at 9.792353996
1255_g_at 9.002960953
1294_at 10.27014218
1316_at 8.029799963
1320_at 6.77626198
1405_i_at 7.455296545
1431_at 6.370126304
1438_at 7.726360458
1487_at 8.526244754
1494_f_at 7.83512073
1598_g_at 12.10076222
160020_at 8.822108397
1729_at 9.374836043
177_at 7.513171158
1773_at 7.10054813
179_at 9.347805081
1861_at 7.890488749

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.




Supplementary file Size Download File type/resource
GSM182299.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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