|
Status |
Public on Mar 15, 2011 |
Title |
Blood_P12_CMLonTKI_33mos |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
CML, chronic phase on IM
|
Organism |
Homo sapiens |
Characteristics |
tissue: Blood patient: P12 age (years): 69 sex: Male disease status: CML cml stage: chronic therapy: treated with imatinib mesylate (IM) for 33mos
|
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 |
G52
|
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 |
|