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Sample GSM182291 Query DataSets for GSM182291
Status Public on Apr 17, 2007
Title Microdissected area # 2 of 1589 tumor
Sample type RNA
Source name Frozen borderline ganglioneuroma maturing tumor
Organism Homo sapiens
Characteristics Phenotype: Borderline ganglioneuroma maturing with areas of schwannian stromal 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 # 2 of 1589 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 7.828151517
1053_at 4.924771578
117_at 5.657030497
121_at 8.109070592
1255_g_at 5.069315697
1294_at 6.978410113
1316_at 6.076067674
1320_at 5.161548028
1405_i_at 5.69330609
1431_at 4.495009014
1438_at 6.194536397
1487_at 6.448805315
1494_f_at 6.523709522
1598_g_at 8.717468322
160020_at 7.309079552
1729_at 6.99864493
177_at 5.361609019
1773_at 5.378482172
179_at 8.058896582
1861_at 5.563751061

Total number of rows: 22283

Table truncated, full table size 496 Kbytes.

Supplementary file Size Download File type/resource
GSM182291.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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