|
| Status |
Public on Jan 01, 2010 |
| Title |
T4-3 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
input, astrocytoma T4-3
|
| Organism |
Homo sapiens |
| Characteristics |
fraction: input
stage: stage 4
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard phenol/chloroform method was used for DNA extraction. The MIRA procedure was as described in Rauch et al., 2006. Cancer Research 66:7939–7947.
|
| Label |
Cy3
|
| Label protocol |
According to NimbleGen Kit
|
| |
|
| Channel 2 |
| Source name |
methylated CpG-island recovery assay (MIRA) enriched, astrocytoma T4-3
|
| Organism |
Homo sapiens |
| Characteristics |
fraction: methylated DNA-enriched
stage: stage 4
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Standard phenol/chloroform method was used for DNA extraction. The MIRA procedure was as described in Rauch et al., 2006. Cancer Research 66:7939–7947.
|
| Label |
Cy5
|
| Label protocol |
According to NimbleGen Kit
|
| |
|
| |
| Hybridization protocol |
According to NimbleGen Kit
|
| Scan protocol |
Follow NimbleScan's default using Agilent Scanner
|
| Description |
stage 4-3
Sample 21
|
| Data processing |
The log2 ratio of the input signals for the enriched and input samples that were co-hybridized to the array is computed and scaled to center the ratio data around zero. Scaling is performed by subtracting the bi-weight mean for the log2-ratio values for all features on the array from each log2-ratio value. VALUE is the P value derived from Kolmogorov-Smirnov test using 750bp window size of the Cy5/Cy3 log2 ratio using NimbleScan.
|
| |
|
| Submission date |
Dec 09, 2009 |
| Last update date |
May 27, 2010 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
xwu@coh.org
|
| Organization name |
City of Hope National Medical Center
|
| Department |
Computational and Quantitative Medicine
|
| Street address |
1500 E. Duarte Rd.
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL9771 |
| Series (1) |
| GSE19391 |
CpG island hypermethylation in human astrocytomas |
|
