|
| Status |
Public on Jun 20, 2012 |
| Title |
Acute Lymphoblastic Leukemia Patient 11 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
PALL_bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
age: 5.9 years
disease state: pediatric acute lymphoblastic leukemia (pALL)
risk assessment: medium risk
tissue: bone marrow
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA with high molecular weight was performed using QIAamp DNA extraction kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
Cy5
|
| Label protocol |
3 μg of digested reference genomic DNA and test genomic DNA was differentially labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies). Initially, the DNA was denatured in the presence of the random primer at 95ºC for 3 minutes in a thermomixer and then quickly cooled in ice. The labeling occurred with the addition of fluorescent dye dUTP-cyanine 3 (Reference DNA) and dUTP-cyanine 5 (Test DNA). Incubation took place for 2 hours at 37ºC in a water bath. The unincorporated nucleotides were removed using Microcon YM-30 filter units (Millipore) and the purified labeled DNA was eluted with 1 x TE Buffer pH 8.0.
|
| |
|
| Channel 2 |
| Source name |
Human male genomic DNA (Promega P/N G147A)
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA with high molecular weight was performed using QIAamp DNA extraction kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
Cy3
|
| Label protocol |
3 μg of digested reference genomic DNA and test genomic DNA was differentially labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies). Initially, the DNA was denatured in the presence of the random primer at 95ºC for 3 minutes in a thermomixer and then quickly cooled in ice. The labeling occurred with the addition of fluorescent dye dUTP-cyanine 3 (Reference DNA) and dUTP-cyanine 5 (Test DNA). Incubation took place for 2 hours at 37ºC in a water bath. The unincorporated nucleotides were removed using Microcon YM-30 filter units (Millipore) and the purified labeled DNA was eluted with 1 x TE Buffer pH 8.0.
|
| |
|
| |
| Hybridization protocol |
The labeled and experimental and reference DNAs were then mixed with the presence of Cot-1 DNA and blocking agent. Following centrifugation, the sample mixture were resuspended in 260ul 2X HI-RPM hybridization buffer, heated to 95°C for 5 minutes and incubated for 30 minutes at 37°C to block repetitive elements on the DNA samples. Then, samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. Hybridization was performed for 40 hours at 65°C using Agilent hybridization station. After hybridization, slides were washed sequentially.
|
| Scan protocol |
Slides were scanned on an Agilent G2505B scanner.
|
| Description |
PALL-11
|
| Data processing |
Images were quantified using Agilent Feature Extraction Software v10.7.3.1. Deep analysis, comparison and visualization of the raw genomic data were performed using Agilent’s DNA Analytics v.4.0.76 software.
|
| |
|
| Submission date |
Jun 19, 2012 |
| Last update date |
Jun 20, 2012 |
| Contact name |
Zubaidah Zakaria |
| E-mail(s) |
zubaidah@imr.gov.my
|
| Phone |
0326162708
|
| Fax |
0326162707
|
| URL |
http://www.imr.gov.my
|
| Organization name |
Institute for Medical Research
|
| Department |
Haematology Unit
|
| Lab |
array CGH Lab
|
| Street address |
Jalan Pahang
|
| City |
Kuala Lumpur |
| ZIP/Postal code |
50588 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL4091 |
| Series (1) |
| GSE32897 |
Chromosomal aberrations in ETV6/RUNX1 positive cases using high-resolution 244K oligo-based array-CGH |
|
