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Sample GSM2677266 Query DataSets for GSM2677266
Status Public on Jun 22, 2017
Title 4936: Diagnosis AML
Sample type genomic
 
Channel 1
Source name Bone Marrow
Organism Homo sapiens
Characteristics gender: Male
diagniosis: AML
fab: M2
type 2 molecular aberration: C/EPBĪ± (double mutation)
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using Trizol reagent according to manufacturer's instructions.
Label Cy5
Label protocol 500ng genomic DNA was cut with MseI, generating 200-800bp fragments. These fragments were ligated to linkers and cut with two methylation-sensitive restriction enzymes (BstuI and HpaII), cutting all the unmethylated fragments. Methylated CpG-island fragments were afterwards amplified by linker-PCR. Amplicons were labeled with Cy5 (patient samples) and Cy3 (common reference samples) fluorescent dye using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA).
 
Channel 2
Source name Common Reference Samples
Organism Homo sapiens
Characteristics diagnosis: Normal
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using Trizol reagent according to manufacturer's instructions.
Label Cy3
Label protocol 500ng genomic DNA was cut with MseI, generating 200-800bp fragments. These fragments were ligated to linkers and cut with two methylation-sensitive restriction enzymes (BstuI and HpaII), cutting all the unmethylated fragments. Methylated CpG-island fragments were afterwards amplified by linker-PCR. Amplicons were labeled with Cy5 (patient samples) and Cy3 (common reference samples) fluorescent dye using the BioPrime Array-CGH Genomic Labeling kit (Invitrogen, Carlsbad, USA).
 
 
Hybridization protocol The Oligo aCGH/ChiP-on-chip Hybridization Kit was used according the protocol to hybridize the labeled gDNA onto the microarrays enclosed in the Agilent SureHyb-enabled hybridization chambers. After o/n hybridization, slides were washed according to protocol o/n.
Scan protocol Scanned on an Agilent G2565AA scanner.
Description CpG island array screening
Reference: Please refer to Differential Methylation Hybridization (DMH) protocol by Dr. Tim H. Huang and coworkers. (PMID 18987809: Yan PS, Potter D, Deatherage DE, Huang TH, Lin S., Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.Methods Mol Biol. 2009;507:89-106.)
Data processing Images were quantified using Agilent Feature Extraction Software (V10.5.1.1) for data extraction. The R and Bioconductor statistical environment (version 2.10.0) were used for quality control and LOESS normalization (limma package). No background correction was performed.
 
Submission date Jun 21, 2017
Last update date Jun 22, 2017
Contact name Nicole Larmonie
E-mail(s) n.larmonie@erasmusmc.nl
Phone 107043891
Organization name ErasmusMC
Street address Wytemaweg
City Rotterdam
ZIP/Postal code 30315 CN
Country Netherlands
 
Platform ID GPL9767
Series (1)
GSE100284 Whole-genome DNA methylation profiling of 152 pediatric AML patients

Data table header descriptions
ID_REF
VALUE Log2 transformed methylation ratio of patient sample and normal reference DNA

Data table
ID_REF VALUE
A_17_P16499695 0.39292716
A_17_P05822757 -0.157498926
A_17_P11189908 0.161811337
A_17_P07299116 0.241346362
A_17_P10258961 -0.58452812
A_17_P17240199 -0.249858863
A_17_P08342170 0.521733271
A_17_P15436892 0.756128262
A_17_P07833726 0.224186101
A_17_P00091682 0.163222762
A_17_P16463750 0.236343287
A_17_P17089734 -0.106219679
A_17_P10158439 -0.152677918
A_17_P01900423 0.851694448
A_17_P16857036 -0.872123773
A_17_P17151535 0.475261199
A_17_P10966774 0.112547515
A_17_P05628591 0.211022404
A_17_P16995120 -0.304286538
A_17_P15006868 -0.043542559

Total number of rows: 168906

Table truncated, full table size 4517 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
Processed data are available on Series record

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