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Sample GSM649341 Query DataSets for GSM649341
Status Public on Jun 01, 2011
Title MCF7-CARM1#13-DOX+E2-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: Dox and D2
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 Dox and E2
SOM01VSC
Sample barcode: 5951702
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 527.6286
AB000461 3413.1078
AB000463 584.894
AB000781 287.8917
AB001025 271.1813
AB001328 24.9354
AB002294 4412.7852
AB002308 8261.5995
AB002311 1947.7573
AB002313 3392.0534
AB002360 324.1974
AB002372 52.1433
AB002377 483.91
AB002381 3597.5817
AB002382 16797.099
AB002384 25.8092
AB003177 2355.5399
AB003333 14318.8643
AB004885 1174.9809
AB006589 29.3101

Total number of rows: 47633

Table truncated, full table size 870 Kbytes.




Supplementary file Size Download File type/resource
GSM649341.calls.gz 3.5 Mb (ftp)(http) CALLS
GSM649341.pair.gz 7.6 Mb (ftp)(http) PAIR
Processed data included within Sample table

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