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Sample GSM299987 Query DataSets for GSM299987
Status Public on Jun 25, 2009
Title 9906_P3C01
Sample type RNA
Source name Diagnostic sample, cryopreserved leukemic blood or bone marrow. See sample charateristics for details.
Organism Homo sapiens
Characteristics age in days at diagnosis : 1751
congenital abnormality : None
gender : Female
race : White
WBC, 1000/microliter : 238
MLL : Negative
CNS status : > 5 CSF WBC/ul with blasts on cytospin and/or eye involvement, cranial nerve involvement, parenchymal brain involvement
testicular involvement : Unknown
TEL-AML,t(12;21) : Negative
trisomy 4 and 10 : Negative
E2A-PBX, t(1;19) : Negative
BCR-ABL, t(9;22) : Negative
tissue type : bone marrow
blast count, % of sample, -1=unavailable : 95
sample viability, % of sample, -1=unavailable : 94
amplification set : 3
hybridization set : 9
training or test set : training set
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA was generated from total RNA using the Affymetrix labeling protocol.
Hybridization protocol cRNA was fragmented and hybridized overnight to Affymetrix U133 Plus 2.0 Genechips.
Scan protocol GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G Plus.
Description Diagnostic sample, cryopreserved leukemic blood or bone marrow. See sample charateristics for details.
Data processing The data were analyzed using Microarray Suite version 5.0 (MAS 5.0) in the Affymetrix Gene Chip Operating Software Version 1.4. Probe masking was used; see the supplementary file 9906_TT207_Affymetrix_probe_mask.msk. Otherwise all Affymetrix default parameter settings were used. Global scaling as the normalization method, with the default target intensity of 500, was used.
Submission date Jun 24, 2008
Last update date Aug 28, 2018
Contact name Maurice Murphy
Phone (505) 925 4001
Organization name UNM Health Sciences Center
Department UNM Cancer Center
Lab Willman Lab
Street address 9501 Camino de Salud
City Albuquerque
State/province NM
ZIP/Postal code 87131
Country USA
Platform ID GPL570
Series (1)
GSE11877 Children's Oncology Group Study 9906 for High-Risk Pediatric ALL
Reanalyzed by GSE119087

Data table header descriptions
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 1393.16 A 0.75
AFFX-BioB-M_at 0 No Call -1
AFFX-BioB-3_at 0 No Call -1
AFFX-BioC-5_at 0 No Call -1
AFFX-BioC-3_at 0 No Call -1
AFFX-BioDn-5_at 0 No Call -1
AFFX-BioDn-3_at 0 No Call -1
AFFX-CreX-5_at 34343.2 A 0.75
AFFX-CreX-3_at 0 No Call -1
AFFX-DapX-5_at 6769.07 P 6.02111e-05
AFFX-DapX-M_at 11586.6 P 6.59169e-05
AFFX-DapX-3_at 18812.8 P 4.42873e-05
AFFX-LysX-5_at 733.755 P 0.00010954
AFFX-LysX-M_at 1198.74 P 0.000125108
AFFX-LysX-3_at 2267.49 P 4.42873e-05
AFFX-PheX-5_at 1336.06 P 4.42873e-05
AFFX-PheX-M_at 1904.22 P 4.42873e-05
AFFX-PheX-3_at 2240.21 P 9.4506e-05
AFFX-ThrX-5_at 1985.68 P 7.00668e-05
AFFX-ThrX-M_at 3310.58 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1619 Kbytes.

Supplementary file Size Download File type/resource
GSM299987.CEL.gz 4.1 Mb (ftp)(http) CEL
GSM299987.CHP.gz 359.6 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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