|
| Status |
Public on Jun 22, 2017 |
| Title |
4730: Diagnosis AML |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Bone Marrow
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
diagniosis: AML
fab: M4
type 2 molecular aberration: NUP98-NSD1
|
| 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 |
|
