Transcriptional analysis of the integral plasma membrane proteome of D1 cells stimulated with LPS harvested at different time-pointstranscriptomic dataset
Affymetrix data will be gathered through an integrated Functional Genomics approach to study DC maturation with an unprecedented detail. D1 cells will be stimulated with LPS and harvested at different time-points for GeneChip analysis and for tandem mass spectrometry-based analysis of the integral plasma membrane proteome. A protocol for obtaining highly pure integral membrane proteins has already been set up in the last two months in the lab of Paola Castagnoli in collaboration with the lab of Juri Rappsilber at IFOM.
A pilot project has already been performed on untreated D1 cells and on D1 cells matured for 24 hours with LPS. The two protein sample are currently being analyzed by tandem mass spectrometry by the lab of Juri Rappsilber. Data will be compared with previously collected microarray data.
From a purely immunological perspective, we will identify new genes that change their expression at the cell surface during DC maturation, that may serve as novel maturation markers or that may tell us something new about DC maturation. From a more systems biology perspective, we will determine the amount of correlation between transcriptome and proteome dynamic changes and reconstruct the first transcript-protein network of DC maturation.
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- time point experiment