|
| Status |
Public on Mar 11, 2011 |
| Title |
Patient_OC498 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Pooled Genomic DNA Male
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Male
cell type: Peripheral Blood Lymphocytes
sample type: Pooled Genomic DNA Male
|
| Treatment protocol |
Freshly collected oral tissues from oral cancer patients and peripheral blood lymhocytes from healthy donors were kept at -80°C till DNA was extracted.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by standard phenol chloroform method. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.
|
| Label |
Cy3
|
| Label protocol |
The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). 1 Micrograms of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3 and Cy5 dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields and specific activity.
|
| |
|
| Channel 2 |
| Source name |
Oral Tumor Tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Oral Tumor
age: 52y
gender: Male
site: Gingivobuccal complex
Stage: 4
|
| Treatment protocol |
Freshly collected oral tissues from oral cancer patients and peripheral blood lymhocytes from healthy donors were kept at -80°C till DNA was extracted.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted by standard phenol chloroform method. Quantity and quality of DNA was monitored using NanoDrop-1000 spectrophotometer and by running agarose gel electrophoresis respectively.
|
| Label |
Cy5
|
| Label protocol |
The samples for Comparative Genomic DNA Hybridization were labeled using Agilent Genomic DNA labeling Kit (Part Number: 5190-0453). 1 Micrograms of each sample was digested using Alu1 and Rsa1. This restricted DNA was then labeled with Cy3 and Cy5 dUTP using random primer labeling method. The labeled DNA was then concentrated and quality assessed for yields and specific activity.
|
| |
|
| |
| Hybridization protocol |
5 micrograms of cy3 and cy5 labeled samples were hybridized. Hybridizations were done using the aCGH Hybridization kit of Agilent (Part Number: 5190-0404). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 40 hours
|
| Scan protocol |
The hybridized slides were washed using Agilent aCGH wash buffers (Part No: 5188-5221/22) and scanned using the Agilent Microarray Scanner G2505C
|
| Description |
Biological replicate
|
| Data processing |
The Analysis was done using Agilent DNA Analytics Software. Significant abberations were identified. (CY5 Treated vs. Cy3 Control)
|
| |
|
| Submission date |
Aug 26, 2010 |
| Last update date |
Aug 03, 2012 |
| Contact name |
Manoj Balkrishna Mahimkar |
| E-mail(s) |
[email protected]
|
| 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 |
GPL4093 |
| Series (1) |
| GSE23831 |
Array CGH analysis of Oral Squamous Cell Carcinoma |
|
