Computational protocol: Type I IFN and not TNF, is Essential for Cyclic Di-nucleotide-elicited CTL by a Cytosolic Cross-presentation Pathway

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Protocol publication

[…] BMDC were re-stimulated for 30 min, 2, 6, 24 and 48 h with Ovalbumin (Hyglos, Germany) alone or co-administered with 10 μg/ml CDA, to generate activated cells. Then, total RNA was isolated from collected DCs using Trizol (Invitrogen) and RNeasy Mini cleanup kit (Qiagen, Germany). RNA was quantified using a Nanodrop 1000D spectrophotometer (ThermoScientific, USA) and quality tested with Agilent 2100 Bioanalyser (Agilent Technologies, USA). Microarray data were generated from Affymetrix microarrays. A minimum of triplicate samples were analyzed to reach statistical significance.The CEL files were uploaded into the geneXplain platform () for the following analysis: microarray measurements were normalized using Robust Multi-array Averaging (RMA) () in the package oligo (). Differentially expressed genes (DEGs) were identified using limma () for altogether 30 conditions defined by time point, treatment and age. Each condition was compared with control measurements to calculate fold changes (logFC) and significance of expression differences (adjusted p-values). Heatmaps were created using geneXplain platform. The microarray data discussed in Supplementary Fig. 5 and Table 1 were stored in NCBI's public repository Gene Expression Omnibus (GEO) under accession number GSE101466. […]

Pipeline specifications

Software tools geneXplain platform, limma
Application WGS analysis