|
| Status |
Public on Feb 19, 2010 |
| Title |
D-388 Tumor |
| Sample type |
genomic |
| |
|
| Source name |
liver tissue
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Tumor
tissue: liver
|
| Treatment protocol |
Cirrhotic liver tissue from 16 HCV-cirrhotic patients without concomintant HCC were also procured as well as 20 normal liver samples.
|
| Growth protocol |
Liver tissue from 20 HCV-HCC patients and their corresponding non-tumorous cirrhotic tissues were procured.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was isolated using QIA amp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions. The EZ DNA methylation kit (Zymo Research) was used for bisulfite conversion of all DNA (1 mg) samples.
|
| Label |
Cy3, Cy5
|
| Label protocol |
After bisulfite treatment, the remaining procedures were identical to the GoldenGate genotyping assay, using Illumina-supplied reagents and conditions.
|
| |
|
| Hybridization protocol |
After extension and ligation, the ligated products were amplified using universal primers and hybridized to an Illumina GoldenGate Methylation BeadArray Cancer Panel I for interrogating CpG sites. The array hybridization was conducted under a temperature gradient.
|
| Scan protocol |
The sentrix array was scanned using Illumina's BeadArray reader and software.
|
| Description |
Methylated channel=Cy3; Unmethylated=Cy5
Proportion methylated
|
| Data processing |
Background was estimated separately for the methylated and unmethylated states as the average intensity of the negative control beads for the red (Rbi) and green channels (Gbi), respectively, and was then subtracted from the beadtype intensities on array i. The maximum of the background subtracted intensities and 0 was then used to calculate the proportion methylated.
|
| |
|
| Submission date |
Sep 11, 2009 |
| Last update date |
Feb 19, 2010 |
| Contact name |
Kellie J. Archer |
| E-mail(s) |
archer.43@osu.edu
|
| Phone |
(614) 247-6167
|
| Organization name |
Ohio State University
|
| Department |
Division of Biostatistics
|
| Street address |
1841 Neil Ave
|
| City |
Columbus |
| State/province |
OH |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL9183 |
| Series (1) |
| GSE18081 |
CpG site methylation of HCV-cirrhotic, HCV-HCC, and normal liver tissues |
|
