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Sample GSM267460 Query DataSets for GSM267460
Status Public on Sep 23, 2009
Title breast cancer DNA hypermethylome: TSA vs mock in T-47D
Sample type RNA
 
Channel 1
Source name Mock treated T-47D cells
Organism Homo sapiens
Characteristics T-47D human breast cancer cell line
Biomaterial provider ATCC
Treatment protocol 1x PBS for 96 hours
Growth protocol McCoy's 5A medium with 10% BCS and 1x P/S
Extracted molecule total RNA
Extraction protocol TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment
Label Cy3
Label protocol Agilent low RNA input linear amplification kit
 
Channel 2
Source name TSA treated T-47D cells
Organism Homo sapiens
Characteristics T-47D human breast cancer cell line treated with TSA
Biomaterial provider ATCC
Treatment protocol 300 nanomolar TSA for 18 hour
Growth protocol McCoy's 5A medium with 10% BCS and 1x P/S
Extracted molecule total RNA
Extraction protocol TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment
Label Cy5
Label protocol Agilent low RNA input linear amplification kit
 
 
Hybridization protocol Agilent Gene Expression Hybridization Kit using manufacturer's protocol (G4140-90050)
Scan protocol Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays. with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.
Description Identification of the breast cancer DNA hypermethylome revealed by gene expression profiling: TSA vs mock in T-47D
Data processing Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor
 
Submission date Feb 22, 2008
Last update date Sep 24, 2008
Contact name Leander Van Neste
Organization name Ghent University
Department Molecular Biotechnology
Lab Bioinformatics and Computational Genomics
Street address Coupure Links 653
City Ghent
ZIP/Postal code 9000
Country Belgium
 
Platform ID GPL4133
Series (1)
GSE10613 Convergence of Mutation and Epigenetic Alterations Identifies Common Target Genes in Breast and Colon Cancer

Data table header descriptions
ID_REF
VALUE Normalized log ratio data: log2(CH2/CH1)
CH1_SIG_MEDIAN Median spot value of channel 1
CH1_BKD_MEDIAN Background median spot value of channel 1
CH2_SIG_MEDIAN Median spot value of channel 2
CH2_BKD_MEDIAN Background median spot value of channel 2

Data table
ID_REF VALUE CH1_SIG_MEDIAN CH1_BKD_MEDIAN CH2_SIG_MEDIAN CH2_BKD_MEDIAN
1 0.237905095128968 37306.7 45 118928 59
2 0.109065977135282 78 45 75 59
3 0.0264358996836066 83 45 79 60
4 -0.0521817249497522 83 46 72 59
5 0.127039954764586 79 46 79 59
6 -0.00428298290289819 82 45 74 59
7 0.0195457998693296 81.5 46 75 59
8 0.0924808321323814 79.5 45 77 60
9 0.0402759688570837 82 45 78 61
10 -0.0176489162889999 83 45 75 59
11 0.0851695816515212 80 46 77.5 60
12 -0.793690014720301 1077.5 45 1326.5 60
13 -0.764880011430788 162.5 46 143 60
14 -0.272080220572896 399.5 45 680.5 60
15 -0.166563545267434 169 45 261 60
16 0.143685081479325 7620 45 19139 60
17 -0.0149511371598590 158.5 46 270.5 58
18 0.133097200576497 251 45 547 59
19 0.683923584374923 31397.8 46 136086 60
20 0.0154507128465802 163 46 289 59

Total number of rows: 45220

Table truncated, full table size 1795 Kbytes.




Supplementary file Size Download File type/resource
GSM267460.txt.gz 11.6 Mb (ftp)(http) TXT
Processed data included within Sample table
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