|
| Status |
Public on Aug 31, 2012 |
| Title |
UC_0497_1 |
| Sample type |
genomic |
| |
|
| Source name |
Bladder tumor UC_0497_1
|
| Organism |
Homo sapiens |
| Characteristics |
bisulfite batch: 4
tissue type: Bladder tumor
tumor stage: T1
tumor grade: 3
Sex: M
age: 75
|
| Treatment protocol |
Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resection at hospitals within the southern healthcare region of Sweden.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using DNeasy spin columns (QIAGEN) acording to manufacturers specifications
|
| Label |
biotin
|
| Label protocol |
According to manufacturers specifications
|
| |
|
| Hybridization protocol |
According to manufacturers specifications
|
| Scan protocol |
According to manufacturers specifications
|
| Description |
UC_0497_1
|
| Data processing |
Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly. Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly. Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly. Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly. Probe-specific background was estimated using the unmethylated channel from hybridizations of SssI methylated control DNAs, and then subtracted from the data to obtain M´ and U´. Values below zero were set back to zero and 2524 sites with (mean (M´+U´)) < 3000 were removed from the data. Beta values were calculated as ß=M´/(M´+U´). Missing values were imputed using k-nearest neighbor imputation (k=10). A batch effect induced by bisulfite-treatment was observed in PCA, and the data was adjusted accordingly.
Normalized Average Beta with replicate samples UC_0556_1.B1, B2 and B3 as well as hybridization controls removed.
Unmethylated and methylated signal intensities in 'signals' matrix which is linked as supplementary file on the Series record.
|
| |
|
| Submission date |
Nov 07, 2011 |
| Last update date |
Aug 31, 2012 |
| Contact name |
Mattias Aine |
| E-mail(s) |
mattias.aine@med.lu.se
|
| Phone |
+46-46-2220394
|
| Organization name |
Lund University
|
| Department |
Oncology
|
| Lab |
Urothelial Cancer Genomics
|
| Street address |
Klinikgatan 28
|
| City |
Lund |
| ZIP/Postal code |
SE-221 84 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL8490 |
| Series (1) |
| GSE33510 |
DNA methylation analyses of urothelial carcinoma reveal distinct epigenetic subtypes and an association between gene copy number and methylation status |
|
