Abstract
Understanding the cellular pathways activated by elevated intraocular pressure (IOP) is crucial for the development of more effective glaucoma treatments. 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. 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. 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. 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. 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.
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Acknowledgments
The National Institutes of Health Grants: 3 R01EY010145-17S1 (DCL); The US-UK Fulbright Commission in conjunction with Fight for Sight; The Special Trustees of Moorfields Eye Hospital (in conjunction with the National Institute for Health Research award to Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology for a Biomedical Research Centre for Ophthalmology) (HJ); R01EY010145 (JCM); P30EY010572 (OHSU Core Grant); and an unrestricted grant from Research to Prevent Blindness (RPB), Inc. JCM is a past RPB Senior Investigator. Short read sequencing assays were performed by the Oregon Health & Science University Massively Parallel Sequencing Shared Resource.
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Lozano, D.C., Choi, D., Jayaram, H., Morrison, J.C., Johnson, E.C. (2018). Utilizing RNA-Seq to Identify Differentially Expressed Genes in Glaucoma Model Tissues, Such as the Rodent Optic Nerve Head. In: Jakobs, T. (eds) Glaucoma. Methods in Molecular Biology, vol 1695. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7407-8_20
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DOI: https://doi.org/10.1007/978-1-4939-7407-8_20
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