|
| Status |
Public on Jun 09, 2010 |
| Title |
TAX577421 |
| Sample type |
genomic |
| |
|
| Source name |
breast tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: breast tumor
family status: sporadic
er: er_neg
pgr: pgr_neg
overall survival time: 722
overall survival event: 1
hu subtype: Basal
spfpercent: 15
nodestatus: node_neg
grade: 3
hc_cluster: 1
fga: 0.21
ezh2_gain: NoGain
sizemm: 23
sizestatus: 2
ageyear: 44
agestatus: 1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated from fresh frozen primary breast tumours in a three-step procedure. Tumour cells were pre-treated with Proteinase K (20 mg/ml) at 55C over-night, DNA was further purified using the Promega Wizard Genomic DNA Purification kit (Promega Corporation, Madison, Wisconsin) and finally DNA was purified by phenol/chloroform treatment in phase-lock tubes.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina GoldenGate Methylation Cancer Panel I using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
breast tumor
|
| Data processing |
The average beta values were obtained according to standard protocols using Illumina BeadStudio Methylation software (version 3.1.3.0).
|
| |
|
| Submission date |
Jun 08, 2010 |
| Last update date |
Jun 09, 2010 |
| Contact name |
Johan Staaf |
| Organization name |
SCIBLU - Swegene Centre for Integrative Biology at Lund University
|
| Street address |
Medicon Village
|
| City |
Lund |
| ZIP/Postal code |
SE-223 81 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL9183 |
| Series (1) |
| GSE22210 |
Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns |
|
