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Sample GSM299959 Query DataSets for GSM299959
Status Public on Jun 25, 2009
Title 9906_P2F07
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 : 5925
congenital abnormality : None
gender : Female
race : Hispanic or Latino
WBC, 1000/microliter : 19.5
MLL : Negative
CNS status : No CNS disease
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 : 71
amplification set : 2
hybridization set : 7
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
E-mail(s) mmurphy@hpc.unm.edu
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
Relations
Reanalyzed by GSE119087

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

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 688.745 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 13619.5 A 0.75
AFFX-CreX-3_at 0 No Call -1
AFFX-DapX-5_at 9430.29 P 5.16732e-05
AFFX-DapX-M_at 15667.5 P 6.59169e-05
AFFX-DapX-3_at 25599.1 P 4.42873e-05
AFFX-LysX-5_at 1115.03 P 5.16732e-05
AFFX-LysX-M_at 1635.61 P 6.59169e-05
AFFX-LysX-3_at 3152.25 P 9.4506e-05
AFFX-PheX-5_at 2081.97 P 4.42873e-05
AFFX-PheX-M_at 2928.09 P 4.42873e-05
AFFX-PheX-3_at 2634.2 P 4.42873e-05
AFFX-ThrX-5_at 2964.92 P 4.42873e-05
AFFX-ThrX-M_at 4939.46 P 4.42873e-05

Total number of rows: 54675

Table truncated, full table size 1629 Kbytes.




Supplementary file Size Download File type/resource
GSM299959.CEL.gz 4.4 Mb (ftp)(http) CEL
GSM299959.CHP.gz 354.3 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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