|
| Status |
Public on Jul 25, 2014 |
| Title |
tumor sample Fumi29b |
| Sample type |
genomic |
| |
|
| Source name |
tumor sample before treatment with 5-fluorouracil
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
tissue type: breast tumor
responder (1: responder,2:nonresponder,9:NA): 1
tp53 (0: wt, 1:mut,9:NA): 0
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated using standard phenol/chloroform procedure
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
genomic DNA from breast tumors
|
| Data processing |
Data processing was performed using BeadStudio. All targets that contained a “zero” value in one sample for methylated and unmethylated signals were removed (n=10). Second, intra-sample normalization, which consists of colour bias and background level correction, was performed using the lumi R package. Subsequently, quantile normalization was performed for between sample normalization. After preprocessing, seven paired samples treated with doxorubicin were excluded due to low methylation levels, resulting in 26 paired tumor samples that were further analyzed. Beta values were used for further analysis.
|
| |
|
| Submission date |
Jul 24, 2014 |
| Last update date |
Jul 25, 2014 |
| Contact name |
Jovana Klajic |
| E-mail(s) |
jovjov@rr-research.no
|
| Organization name |
OUS/Radium Hospital
|
| Department |
Genetics
|
| Street address |
Ullernchauseen 70
|
| City |
Oslo |
| ZIP/Postal code |
0379 |
| Country |
Norway |
| |
|
| Platform ID |
GPL8490 |
| Series (1) |
| GSE59724 |
Methylation analysis of locally advanced breast tumors treated with two drugs-doxorubicin and 5-fluorouracil |
|
