Gene expression profiling of epidermal cell types in C. elegans using Targeted DamID

In this study we use targeted DamID to assay RNA polymerase occupancy across the genome specifically within the seam cells and hypodermis of C. elegans to identify genes expressed in these cell-types. Overall design: Identification of sets of expressed genes within the seam cells and the hypodermis of C. elegans by cell-type-specific expression of a DAM:RPB-6 fusion using the seam cell promoter srf-3i1 and the hypodermal promoter dpy-7syn1. DAM:RPB-6 occupancy across the genome is assayed in the form of GATC 6mA methylation in comparison to that of an equivalent control DAM:NLS-GFP fusion and genes with significant levels of occupancy are identified. Two biological replicates were aquired for every fusion and cell-type at each of the L2 and L4 developmental stages.