Transcriptomics is defined as the analysis of the complete set of RNA transcripts present in a cell under different circumstances, quiescent versus challenge, by microarray analysis. Comparison of transcriptomes identifies genes that are differentially expressed in different cell populations under different conditions. In this paper deep RNA sequencing (RNA-Seq) was performed on human, adult and foetal, trabecular meshwork (TM) cornea and ciliary body (CB) tissue to analyse expression of genes associated with various clinical features. There were on average over 12,000 protein coding genes and 3725 novel transcripts expressed in each tissue. Top rated genes included secreted protein acidic and cysteine rich (SPARC) encoding a cysteine-rich acidic matrix-associated protein in foetal cornea and TM, clusterin (Clu), a secreted chaperone that can under some stress condition in adult cornea, and prostaglandin D2 synthase (PTGDS) which catalyses the conversion of prostaglandin H2 (PGH2) to prostaglandin D2 (PGD2). In a candidate approach expression mRNA for 29 genes associated with primary open-angle glaucoma showed that most were present in the tissues investigated supporting a role in the condition. Finally, differential expression of many genes was seen when comparing foetal and adult tissues. This study describes the transcriptome and potentially protein production in several ocular tissues. The results provide a resource for future studies including comparison of expression in different tissues and the effect of challenge, inflammation or infection, on this expression.