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Sample GSM552812 Query DataSets for GSM552812
Status Public on Jun 09, 2010
Title TAX577210
Sample type genomic
 
Source name breast tumor
Organism Homo sapiens
Characteristics tissue: breast tumor
family status: brca2
er: er_pos
pgr: pgr_neg
overall survival time: 2126
overall survival event: 1
hu subtype: LumB
spfpercent: 9
nodestatus: node_pos
grade: 3
hc_cluster: 1
fga: 0.64
ezh2_gain: NoGain
sizemm: 34
sizestatus: 2
ageyear: 58
agestatus: 2
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

Data table header descriptions
ID_REF
VALUE Average beta value

Data table
ID_REF VALUE
AATK_E63_R 0.9742068
AATK_P709_R 0.9674325
ABCA1_E120_R 0.01781922
ABCA1_P45_F 0.005120533
ABCB4_E429_F 0.9935911
ABCB4_P51_F 0.9943267
ABCB4_P892_F 0.2416804
ABCC2_E16_R 0.5785459
ABCC2_P88_F 0.992816
ABCC5_P444_F 0.009215213
ABCG2_P178_R 0.04153851
ABCG2_P310_R 0
ABL1_P53_F 0.1278733
ABL2_P459_R 0.02326627
ABO_E110_F 0.0263169
ABO_P312_F 0.06023798
ACTG2_E98_R 0.985908
ACTG2_P346_F 0.9318209
ACTG2_P455_R 0.9922299
ACVR1_E328_R 0.9244095

Total number of rows: 1452

Table truncated, full table size 31 Kbytes.




Supplementary data files not provided
Processed data not applicable for this record

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