TBX3 whole genome microarray dataset
Description
Differential gene expression when TBX3 is knocked down in ME1402 vertical growth phase melanoma.
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Gene expression profiling was performed using the Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A). Total RNA from ME1402 shCtrl and shTBX3 cell lines was reverse transcribed to cDNA using the One-Color RNA Spike-In Kit (5188-5282), followed by an in vitro transcription reaction to amplify and label complementary RNA (cRNA) with Cy3-CTP using the Low Input Quick Amp Labeling Kit (5190-2305). Cy3-labeled cRNA was hybridized to the microarray chips using the Gene Expression Hybridization Kit (5188-5242). Microarray slides were scanned on a dynamic autofocus Agilent G2565BA microarray scanner. The processed Multiplicative Detrend FE data (FE v9.4.1, GE1-v5_91_0806 protocol) was median normalised and missing values were inputed (Limma and impute, R packages). Significance in differential gene expression was determined using standard Student's t test of two groups. Adjusted P values were computed by controlling the false discovery rate (FDR) with the Benjamini & Hochberg (BH) procedure implemented in multi-test (R package). Differentially expressed genes were defined as follows: BH adjusted p value <0.05 and absolute mean log2 ratio greater than one (fold change≥2). The use of this datasets requires permission from the corresponding author upon request.