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Sample GSM299897 Query DataSets for GSM299897
Status Public on Jun 25, 2009
Title 9906_P1E09
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 : 6511
congenital abnormality : None
gender : Male
race : White
WBC, 1000/microliter : 515
MLL : Positive
CNS status : No CNS disease
testicular involvement : Negative
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 : peripheral blood
blast count, % of sample, -1=unavailable : 95
sample viability, % of sample, -1=unavailable : 99
amplification set : 1
hybridization set : 3
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 595.126 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 520.42 A 0.25
AFFX-CreX-3_at 0 No Call -1
AFFX-DapX-5_at 3225.16 P 4.42873e-05
AFFX-DapX-M_at 6472.41 P 6.59169e-05
AFFX-DapX-3_at 11371.1 P 4.42873e-05
AFFX-LysX-5_at 435.135 P 0.000195116
AFFX-LysX-M_at 647.099 P 6.59169e-05
AFFX-LysX-3_at 1435.2 P 7.00668e-05
AFFX-PheX-5_at 812.716 P 5.16732e-05
AFFX-PheX-M_at 1049.86 P 4.42873e-05
AFFX-PheX-3_at 1170.98 P 4.42873e-05
AFFX-ThrX-5_at 1196.98 P 5.16732e-05
AFFX-ThrX-M_at 1681.9 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1641 Kbytes.

Supplementary file Size Download File type/resource
GSM299897.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM299897.CHP.gz 349.0 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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