|
| Status |
Public on Apr 26, 2017 |
| Title |
Patient_OPL_OC2293 |
| 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).
|
| |
|
| Channel 2 |
| Source name |
OC2293_Cy5
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: Oral leukoplakia
tissue: Oral
age: 33y
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 |
|
