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Series GSE39141 Query DataSets for GSE39141
Status Public on Nov 07, 2012
Title Genome-wide DNA methylation profiling predicts relapse in childhood B-cell acute lymphoblastic leukemia
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Although the 5-year survival of childhood Acute Lymphoblastic Leukemia (ALL) exceeds 80%, a group of patients presents poor prognosis due to early relapse. To date, treatment strategies are defined by cytogenetically-based subtype categorization. However, ALL patients without chromosomal translocations associated with poor prognosis lack diagnostic markers to adjust specific therapies. DNA methylation alteration is a frequent event in cancer with high potential in diagnosis, prognosis and prediction of drug response. Hence, we aimed to characterize childhood B-ALLs without Philadelphia (BCR-ABL) and MLL translocations based on their DNA methylation profile of more than 450,000 CpG sites to improve accuracy in prognosis and treatment strategies.
 
Overall design DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was performed according to the manufacturer's recommendation for the Illumina Infinium Assay. Effective bisulfite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite-converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following the Illumina Infinium HD Methylation protocol. Chip analysis was performed using the Illumina HiScan SQ fluorescent scanner. The intensities of the images were extracted using GenomeStudio (2010.3) Methylation module (1.8.5) software. The methylation score of each CpG is represented as a beta value.
 
Contributor(s) Sandoval J, Esteller M
Citation(s) 23110451
Submission date Jul 05, 2012
Last update date Mar 22, 2019
Contact name Manel Esteller
Organization name IDIBELL
Department PEBC
Lab Cancer Epigenetics
Street address Hospital Duran i Reynals Av. Gran Via s/n km, 2.7
City L'Hospitalet de Llobregat
State/province Barcelona
ZIP/Postal code 08908
Country Spain
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (33)
GSM956761 Bone marrow mononuclear cells, 02_1505
GSM956762 Bone marrow mononuclear cells, 07_2252
GSM956763 Bone marrow mononuclear cells, 03_1310
Relations
BioProject PRJNA170081

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE39141_RAW.tar 183.1 Mb (http)(custom) TAR
Processed data included within Sample table
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