Computational protocol: Global comparative transcriptome analysis of cartilage formation in vivo

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Protocol publication

[…] Interrogation of the 11.5 dpc, 12.5 dpc, and 13.5 dpc cRNA samples by microarray analysis involved a saturated hybridization strategy with dye swaps. Thus, cRNA samples from each time point were labelled with both Cy3 and Cy5 fluorophores, and six hybridizations were performed such that each time point was compared with each other time point using both dye combinations (to normalize against dye biases). 44 K whole mouse genome microarrays (G4122F, ID014868, Agilent) were hybridized according to the manufacturer's instructions. The arrays were then scanned at 10 μm resolution on an Axon 4000B scanner and the features acquired with the GenePix Pro 4.1 software (Axon Instruments). The raw data was then processed using a print-tip loess normalization [] using limmaGUI [,] which is an implemented package of R used to fit linear models to microarray data . Genes were ranked according to their differential expression and gene lists were generated based on biological process and function (GOStat and OntoExpress). […]

Pipeline specifications

Software tools GenePix Pro, limmaGUI, GOstat, Onto-Express
Application Gene expression microarray analysis
Organisms Mus musculus