RNA-Seq analysis and comparison of corneal epithelium in keratoconus and myopia patients

We compared the transcriptome of keratoconus and control epithelium using RNA-Seq. Epithelial tissues were obtained prior to surgery from keratoconus and myopia control patients, undergoing collagen cross-linking and photorefractive keratectomy, respectively. We identified major differences in keratoconus linked to cell-cell communication, cell signalling and cellular metabolism. The genes associated with the Hedgehog, Wnt and Notch1 signaling pathways were down-regulated in keratoconus. Twenty samples were used for RNA-Seq including 10 KC and 10 controls. All 10 KC samples were from males, and there were 4 samples from females in the control group. Samples were prepared and processed in 2 batches each with 5 control samples and 5 KC samples. The RNA samples were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina,USA) according to the manufacturer’s instructions. The libraries were sequenced on a NextSeq500 (Illumina) using a 75bp paired end read high output v2 run at the Ramaciotti Centre for Genomics UNSW.