|
| Status |
Public on Jun 01, 2008 |
| Title |
EAC tumor biopsy from 40334 |
| Sample type |
genomic |
| |
|
| Source Name |
Esopageal Adenocarcinoma Tumor Biopsy
|
| Organism(s) |
Homo sapiens |
| Characteristics |
Biopsy taken by endoscopy prior to treatment. Subject details
Gender: male
Age: 68 years
Tissue: EAC tumor
Tumor stage: IIA
|
| Treatment protocol |
Fresh tissue was placed directly into RNAlater solution, stored at 4°C overnight, then -20°C. Long-term storage was then at -80°C after access RNAlater was removed.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
As per QIAGEN tissue lyser protocol using ALLPREP Kit
|
| Label |
C-Bio and A-DNP
|
| Label protocol |
The Infinium II assay was done using Illumina Sentrix HumanHap300 genotyping BeadChip arrays (317K, TagSNP Phase I, v1.1) according to the manufacturer's specifications (Illumina, San Diego, CA). Briefly, 750 ng of genomic DNA were amplified at 37°C overnight, using solutions WG-AMM and WG-MP1. After overnight incubation, the amplified DNA was fragmented using WG-FRG and precipitated with isopropanol after the addition of WG-PA1.
|
| |
|
| Hybridization protocol |
The dried precipitated pellet was then resuspended in WG-RA1 and hybridized to a beadchip along with WG-RA1 and formamide. The arrays were then incubated overnight at 48°C, after which they underwent single-base extension on a Teflow chamber rack system (Tecan, Männedorf, Switzerland) using WG-XC1, WG-XC2, and WG-TEM.
|
| Scan protocol |
After the single-base extension step, the beadchips were stained with WG-LTM and WG-ATM, dried for 1 h, then imaged using a BeadArray Reader (Illumina).
|
| Description |
The EAC biopsies used in this study were collected as part of the Australian Cancer Study.
|
| Data processing |
Image data was analyzed using Beadstudio 2.0 (Illumina). EAC samples log_R_ratio values were generated using the squamous sample 192R as a reference. All genomic positions were based upon hg17 from the UCSC Genome Browser.
|
| |
|
| Submission date |
Feb 13, 2008 |
| Contact name |
Derek John Nancarrow |
| E-mail(s) |
derek.nancarrow@qimr.edu.au
|
| Phone |
61 7 3362 0323
|
| Fax |
61 7 3845 3508
|
| Organization name |
Queensland Institute of Medical Research
|
| Department |
Genetics & Population Health
|
| Lab |
Oncogenomics
|
| Street address |
300 Herston Road
|
| City |
Herston |
| State/province |
Queensland |
| ZIP/Postal code |
4006 |
| Country |
Australia |
| |
|
| Platform ID |
GPL5711 |
| Series (1) |
| GSE10506 |
Genome-wide analysis of esopageal adenocarcinoma tumor biopsy using high-density single-nucleotide polymorphism arrays. |
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