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Sample GSM127858 Query DataSets for GSM127858
Status Public on Sep 02, 2009
Title Reference_17-50khind
Sample type genomic
 
Source name Pediatric acute lymphoblastic leukemia (ALL) blast samples or reference leukemic blast samples.
Organism Homo sapiens
Characteristics Leukemic blasts from 242 pediatric acute lymphoblastic leukemia (ALL) patients, or reference leukemic blast samples used for DNA copy number analysis.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label Biotin
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description 242 pediatric acute lymphoblastic leukemia blast samples were analyzed.
Data processing CEL files were generated using GeneChip Operating Software v 3.0 and SNP calls generated using GeneChip DNA Analysis Software (GDAS) v 3.0 or Affymetrix GeneChip Genotyping Analysis Software (GTYPE) v 4.0. The summary files (containing both expression values and SNP calls) were generated by dChipSNP, and a modified array normalization algorithm that accounts for gross cytogenetic abnormalities in the blast samples (described in the paper).
 
Submission date Aug 14, 2006
Last update date Dec 22, 2009
Contact name Charles G Mullighan
E-mail(s) charles.mullighan@stjude.org
Phone 1-901-595-3387
Organization name St Jude Children's Research Hospital
Department Pathology
Street address 262 Danny Thomas Place
City Memphis
State/province TN
ZIP/Postal code 38105
Country USA
 
Platform ID GPL2004
Series (1)
GSE5511 Genes regulating B cell development are mutated in acute lymphoid leukaemia

Supplementary data files not provided
Processed data not provided for this record

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