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Sample GSM388431 Query DataSets for GSM388431
Status Public on Dec 14, 2009
Title AP-2 gamma targetting siRNA 3: CCACACUGGAGUCGCCGAAUA Technical Replicate 2
Sample type RNA
 
Source name siRNA treated MCF-7 breast carcinoma cell line
Organism Homo sapiens
Characteristics protocol: AP-2 gamma targetting siRNA 3
cell line: MCF7
Treatment protocol Cells were transfected (using Oligofectamine; Invitrogen) with 25nM siRNA targetting AP-2gamma or non-silencing control siRNA or no siRNA (transfection reagent only).
Growth protocol MCF-7 cells were cultured in DMEM, 10% FCS; plus insulin (10ug/ml).
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol (Sigma) following the standard protocol but including a Qiagen RNAeasy Mini column (with RNAse free DNAse step) for clean up and elution.
Label biotin
Label protocol Total RNA (8ug) from each sample was used to prepare biotinylated target RNA, using the One Cycle Target Labelling kit (Invitrogen) according to the manufacturer’s recommendations (http://www.affymetrix.com/support/technical/manual/expression_manual.affx)
 
Hybridization protocol 15 ug of cRNA was hybridized for 16 hr at 45C to Human Genome U133 Plus 2.0 oligonucleotide arrays (as described at http://www.affymetrix.com/products/arrays/specific/hgu133plus.affx). Arrays were washed and stained using the Affymetrix Fluidics Station 450.
Scan protocol Arrays were scanned using an Affymetrix GeneArray 3000 scanner. Array images were assessed by eye to confirm scanner alignment, the absence of significant bubbles or scratches, and a low background.
Description AP-2 gamma silenced
Data processing The data were pre-processed using the “affy” package in BioConductor: “mas5” background correction, “quantiles” normalisation (Bolstad et al. 2003), “pmonly” correction and “medianpolish” summarisation. The resulting log2 scale transformed data were imported into the Genespring package (Genespring GX 7.3, Agilent Technologies) and filtered to retain the 2500 probe sets with the highest variance across all the arrays. Welch’s t-test was then applied in conjunction with a False Discovery Rate (FDR) multiple test correction to identify the most significantly regulated genes (p<0.01).
 
Submission date Mar 31, 2009
Last update date Aug 28, 2018
Contact name Helen C Hurst
E-mail(s) [email protected]
Organization name Institute of Cancer
Department Centre for Tumour Biology
Street address Charterhouse Square
City London
ZIP/Postal code EC1M 6BQ
Country United Kingdom
 
Platform ID GPL570
Series (1)
GSE15481 Gene expression data from AP-2γ silenced MCF-7 cells
Relations
Reanalyzed by GSE119087

Data table header descriptions
ID_REF
VALUE log2 scale normalised data

Data table
ID_REF VALUE
1007_s_at 12.15488842
1053_at 9.524030627
117_at 7.715443906
121_at 9.473589638
1255_g_at 5.754960715
1294_at 8.198865598
1316_at 7.237289675
1320_at 7.161286852
1405_i_at 7.930123887
1431_at 5.85574629
1438_at 7.838760645
1487_at 9.175579986
1494_f_at 7.150930715
1552256_a_at 9.608034224
1552257_a_at 8.617457963
1552258_at 6.867539081
1552261_at 7.103062759
1552263_at 6.428626284
1552264_a_at 8.429690761
1552266_at 6.839526221

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM388431.CEL.gz 8.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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