|
| Status |
Public on Mar 15, 2011 |
| Title |
Blood_P8_CMLonTKI_45mos |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
CML, chronic phase on IM
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
patient: P8
age (years): 60
sex: Male
disease status: CML
cml stage: chronic
therapy: treated with imatinib mesylate (IM) for 45mos
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted from archived samples using QIAGEN AllPrep® DNA/RNA/Protein Mini Kit, as recommended by the manufacturer.
|
| Label |
Cy5
|
| Label protocol |
1.0µg of total genomic DNA (gDNA) of the test sample (patient) and a references sample with concentration at least 50ng/µL were digested with 5U of AluI and RsaI for 2h at 37°C followed by incubation for 20 minutes at 65°C to inactivate the enzymes. The purified restricted samples were labeled with Cy5-dUTP or Cy3-dUTP by using the Agilent genomic DNA labeling kit PLUS (Agilent p/n 5188-5309) as per manufacturers instructions. Both purified labeled genomic DNA were combined.
|
| |
|
| Channel 2 |
| Source name |
Human male genomic DNA (Promega P/N G1471)
|
| Organism |
Homo sapiens |
| Characteristics |
sex: Male
reference: Promega P/N G1471
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was extracted from archived samples using QIAGEN AllPrep® DNA/RNA/Protein Mini Kit, as recommended by the manufacturer.
|
| Label |
Cy3
|
| Label protocol |
1.0µg of total genomic DNA (gDNA) of the test sample (patient) and a references sample with concentration at least 50ng/µL were digested with 5U of AluI and RsaI for 2h at 37°C followed by incubation for 20 minutes at 65°C to inactivate the enzymes. The purified restricted samples were labeled with Cy5-dUTP or Cy3-dUTP by using the Agilent genomic DNA labeling kit PLUS (Agilent p/n 5188-5309) as per manufacturers instructions. Both purified labeled genomic DNA were combined.
|
| |
|
| |
| Hybridization protocol |
The purified labeled samples were mixed with 50 μg of human Cot-1 DNA (Invitrogen) and Agilent 10X Blocking Agent and Agilent 2X Hybridization Buffer. The hybridization mixtures were denatured at 95°C for 3 min and incubated at 37°C for 30 min. Samples were then applied to the microarrays enclosed in Agilent SureHyb-enabled hybridization chambers for 24 h at 65°C. After hybridization, slides were washed sequentially.
|
| Scan protocol |
Slides were scanned on an Agilent G2505B scanner.
Microarray images were processed using Agilent Feature Extraction Software (version 9.5.31).
|
| Description |
G122
|
| Data processing |
Linear normalized background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.
Normalized log2ratio (Cy5/Cy3) or (Cy3/Cy5) representing CML/ref is provided in the data matrix.
|
| |
|
| Submission date |
Sep 02, 2010 |
| Last update date |
Feb 08, 2012 |
| Contact name |
Veera Sekaran Nadarajan |
| E-mail(s) |
veera@um.edu.my
|
| Fax |
60379494639
|
| Organization name |
University Malaya
|
| Department |
Pathology
|
| Lab |
Molecular and Genetic Analysis
|
| Street address |
Lembah Pantai
|
| City |
Kuala Lumpur |
| State/province |
W.P. |
| ZIP/Postal code |
50603 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL5477 |
| Series (1) |
| GSE23946 |
Identification of copy number alterations by array comparative genomic hybridization in patients with late chronic or accelerated phase chronic myeloid leukemia treated with imatinib mesylate |
|
