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Sample GSM649339 Query DataSets for GSM649339
Status Public on Jun 01, 2011
Title MCF7-CARM1#13-DMSO-a
Sample type RNA
 
Source name breast cancer cell line
Organism Homo sapiens
Characteristics cell type: breast cancer cell line
cell line: MCF7-tet-on-CARM1 clone 13
treatment: DMSO
Treatment protocol When the cells were treated with Dox, they were treated with 1ug/ml Dox for 4 days to induce CARM1 expression. The medium were changed to phenol-red free DMEM+charcoal stripped FBS for 2 days before treating with E2 (10nM)
Growth protocol MCF7-tet-on-CARM1 cells were grown in DMEM in 10% FBS. Two days before E2 treatment, the cells were switched to phenol-red free DMEM with 5% 6X charcoal stripped FBS.
Extracted molecule total RNA
Extraction protocol mRNA were extracted from cells using Qiagen Rneasy Kit
Label Cy3
Label protocol Invitrogen SuperScript Double-Stranded cDNA Synthesis Kit was used to synthesize double-stranded cDNA that was going to be labeled using a NimbleGen One-Color DNA Labeling Kit.
 
Hybridization protocol Hybridization was performed at 42C for 20hrs, according to NimbleGen gene expression arrays user’s guide (2010).
Scan protocol One-color NimbleGen arrays were scanned with the MS 200 Microarray Scanner and the data were extract using the MS 200 Data Collection Software.
Description DMSO alone
SOM01VS8
Sample barcode: 5943702
Data processing The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
 
Submission date Jan 05, 2011
Last update date Jun 01, 2011
Contact name Wei Xu
Organization name UW-Madison
Street address 1400 University Ave
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL11219
Series (1)
GSE26454 Gene expression profiles of CARM1 overexpression in MCF7

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000409 327.6825
AB000461 4274.4931
AB000463 429.7412
AB000781 180.8828
AB001025 126.6462
AB001328 33.8794
AB002294 3950.2784
AB002308 10027.7937
AB002311 1537.3943
AB002313 2961.9591
AB002360 262.1244
AB002372 55.7801
AB002377 441.1884
AB002381 2267.046
AB002382 21081.9972
AB002384 18.6494
AB003177 2314.8148
AB003333 15101.958
AB004885 1141.9866
AB006589 34.7102

Total number of rows: 47633

Table truncated, full table size 868 Kbytes.




Supplementary file Size Download File type/resource
GSM649339.calls.gz 3.5 Mb (ftp)(http) CALLS
GSM649339.pair.gz 7.6 Mb (ftp)(http) PAIR
Processed data included within Sample table

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