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Īhmed F, Brown KM, Stephan DA, Morrison JC, Johnson EC, Tomarev SI (2004) Microarray analysis of changes in mRNA levels in the rat retina after experimental elevation of intraocular pressure. Johnson EC, Jia L, Cepurna WO, Doser TA, Morrison JC (2007) Global changes in optic nerve head gene expression after exposure to elevated intraocular pressure in a rat glaucoma model. Johnson EC, Doser TA, Cepurna WO, Dyck JA, Jia L, Guo Y, Lambert WS, Morrison JC (2011) Cell proliferation and interleukin-6-type cytokine signaling are implicated by gene expression responses in early optic nerve head injury in rat glaucoma. Howell GR, Macalinao DG, Sousa GL, Walden M, Soto I, Kneeland SC, Barbay JM, King BL, Marchant JK, Hibbs M, Stevens B, Barres BA, Clark AF, Libby RT, John SW (2011) Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma. The methods described here could also be applied to small tissue samples (less than 100 ng in total RNA yield) from retina, optic nerve, or other regions of the central nervous system. Here, we describe an RNA-seq method specifically developed for identifying differentially expressed genes in optic nerve heads of eyes exposed to elevated intraocular pressure. However, RNA sequencing (RNA-seq) is a powerful tool for investigating known transcripts, as well as for exploring new ones (including noncoding RNAs and small RNAs), is more quantitative, and has the added benefit that the data can be re-analyzed as new sequencing information becomes available. Limitations of microarrays include that they can only be used to detect transcripts that correspond to existing genomic sequencing information and their narrower dynamic range. Microarray studies have previously been used to identify several key gene expression changes in early and extensively injured ONH, as well as in the retina. Understanding the cellular pathways activated by elevated intraocular pressure (IOP) is crucial for the development of more effective glaucoma treatments.