|
Status |
Public on Apr 26, 2017 |
Title |
Patient_OPL_OC2203 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
Male_Pooled_Cy3 control
|
Organism |
Homo sapiens |
Characteristics |
tissue: Peripheral Blood cell type: Lymphocytes
|
Treatment protocol |
Freshly collected oral tissues from oral leukoplakia and oral cancer patients were kept at -80°C till DNA was extracted. Peripheral blood lymhocytes from healthy donors were processed immediately for DNA extraction.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted using AllPrep® DNA/RNA/miRNA Universal kit, QIAGEN. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.
|
Label |
Cy3
|
Label protocol |
1.5µg of tumor and pooled gender-matched reference DNA were labeled with fluorochromes Cy3 and Cy5, respectively using Agilent Sure tag DNA labeling kit (Agilent Technologies, 5190-3400). Labeled samples were purified using the genomic DNA purification module (Agilent Technologies).
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|
|
Channel 2 |
Source name |
OC2203_Cy5
|
Organism |
Homo sapiens |
Characteristics |
diagnosis: Oral leukoplakia tissue: Oral age: 32y gender: Male site: Gingivobuccal complex Stage: Oral Precancer
|
Treatment protocol |
Freshly collected oral tissues from oral leukoplakia and oral cancer patients were kept at -80°C till DNA was extracted. Peripheral blood lymhocytes from healthy donors were processed immediately for DNA extraction.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
DNA was extracted using AllPrep® DNA/RNA/miRNA Universal kit, QIAGEN. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.
|
Label |
Cy5
|
Label protocol |
1.5µg of tumor and pooled gender-matched reference DNA were labeled with fluorochromes Cy3 and Cy5, respectively using Agilent Sure tag DNA labeling kit (Agilent Technologies, 5190-3400). Labeled samples were purified using the genomic DNA purification module (Agilent Technologies).
|
|
|
|
Hybridization protocol |
4.5 µg of purified labelled samples was mixed with human Cot-1 DNA, and denatured at 95°C (Oligo aCGH hybridization kit, Agilent Technologies, 5188-5380). The mixture was applied to Agilent microarrays slides and hybridization was performed at 65°C for 40 hours. After hybridization, the microarrays were washed with Oligo aCGH wash buffer followed by drying of slides.
|
Scan protocol |
Scanned using an Agilent Scanner (Agilent Technologies, G2600D)
|
Description |
Biological replicate
|
Data processing |
Image Analysis was performed using Agilent feature extraction software version 11.5 and Linear Normalization
|
|
|
Submission date |
Aug 11, 2016 |
Last update date |
Apr 26, 2017 |
Contact name |
Manoj Balkrishna Mahimkar |
E-mail(s) |
mmahimkar@actrec.gov.in
|
Phone |
+91-22-27405049
|
Organization name |
Cancer Research Institute, Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre
|
Lab |
Mahimkar Lab
|
Street address |
Sector-22, Owe Village, Kharghar Node
|
City |
Navi Mumbai |
State/province |
Maharashtra |
ZIP/Postal code |
410208 |
Country |
India |
|
|
Platform ID |
GPL22311 |
Series (1) |
GSE85514 |
Array CGH analysis of Oral Leukoplakia and Early Stage Oral Squamous Cell Carcinoma |
|