|
Status |
Public on Jun 22, 2017 |
Title |
8723: Diagnosis AML |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Bone Marrow
|
Organism |
Homo sapiens |
Characteristics |
gender: Female diagniosis: AML fab: M5 type 2 molecular aberration: HLXB9-ETV6
|
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).
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|
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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.
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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 |
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