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Sample GSM90404 Query DataSets for GSM90404
Status Public on Jan 04, 2006
Title 1288 (HG-U95A)
Sample type RNA
 
Source name Primary Tumor
Organism Homo sapiens
Characteristics Age Diagnosis: 1626, INSS Stage:4, MYCN:Amplified, 1p36 LOH:LOH, 11q23 LOH:LOH, Unb11qLOH:No Unbalanced LOH, 17q gain:ND, Tumor %:97
Extracted molecule total RNA
Label Biotin
Label protocol Standard Affymetrix protocol
 
Description Primary neuroblastoma tumor. Tumor annotation : ND is Not Done.
Data processing Statistical modeling of probe set behavior was conducted using Probe Profiler (Corimbia, Berkeley, CA) as described by the manufacturer. The software implements a model-based approach for data extraction from probe sets and weights probe pairs based on consistency of performance. Normalization to remove chip-to-chip variation is accomplished by subtracting the second percentile intensity value and dividing by the interquartile range (IQR). A quantitative expression score (e-score) is then calculated for each probe set.
 
Submission date Jan 03, 2006
Last update date Mar 16, 2009
Contact name Jayanti Jagannathan
E-mail(s) [email protected]
Phone 2674262286
Organization name Childrens Hospital of Philadelphia
Department Oncology
Street address 34th & Civic center blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL8300
Series (1)
GSE3960 Classification of neuroblastoma by integrating gene expression pattern with regional alterations in DNA copy number
Relations
Alternative to GSM174424 (aCGH data from the same sample)

Data table header descriptions
ID_REF
VALUE Probe-Profiler -calculated Signal intensity

Data table
ID_REF VALUE
AFFX-MurIL2_at 13.7272
AFFX-MurIL10_at 17.1609
AFFX-MurIL4_at 1.97952
AFFX-MurFAS_at 8.14893
AFFX-BioB-5_at 273.652
AFFX-BioB-M_at 355.274
AFFX-BioB-3_at 331.652
AFFX-BioC-5_at 672.925
AFFX-BioC-3_at 639.81
AFFX-BioDn-5_at 695.104
AFFX-BioDn-3_at 2678.6
AFFX-CreX-5_at 3938.39
AFFX-CreX-3_at 3852.74
AFFX-BioB-5_st 169.014
AFFX-BioB-M_st 116.809
AFFX-BioB-3_st 24.1396
AFFX-BioC-5_st 101.917
AFFX-BioC-3_st 43.2261
AFFX-BioDn-5_st 411.972
AFFX-BioDn-3_st 158.355

Total number of rows: 12625

Table truncated, full table size 212 Kbytes.




Supplementary file Size Download File type/resource
GSM90404.CEL.gz 2.6 Mb (ftp)(http) CEL

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