Determination of Nir (Noc2l) function in epidermis during mouse development by global transcriptome analysis

To investigate the role of Nir in epidermis during embryogenesis, we crossed mice harboring conditional Nir alleles with the Krt14-Cre deleter strain, which results in Cre-mediated loss of Nir selectively in epidermis. Transciptome analysis of keratinocytes obtained from control and knock-out mice at E15.5 revealed 4393 genes differentially expressed between Nir knock-out and control mice (p-value<10-2). At E17.5, we found 5673 differentially expressed genes. We selectively knocked-out Nir in epidermis by crossing Nir floxed mice to Krt14-Cre mice. At E15.5 and E17.5, epidermis was separated from the dermnis and RNA from control Nir floxed mice) and knock-out mice was extracted with trizol according to the manufacturer protocol. RNA samples were sequenced by the standard Illumina protocol to create raw sequence files (.fastq files). We annotated these reads to the mm10 build of the mouse genome using TopHat version 2. The aligned reads were counted with the homer software (analyze RNA) and DEG’s were identified using EdgeR.