We envision the following as the main experimental strategy for FANTOM6:
- We are generating a reference set of genome-wide profiles to establish the basal state of the transcriptome and epigenome in each cell type.
- We are perturbing a set of lncRNAs in each cell type, and evaluating the molecular phenotype of the perturbation by CAGE profiling followed by bioinformatics analysis. The lncRNAs selected for perturbation are based on published transcripts as well as yet unpublished RNAseq assemblies specific to the cell types in the FANTOM5 collection.
- A selected subset of lncRNAs will be functionally characterized in more detail using other complementary technologies.