Utilizing RNA-seq to identify differentially expressed genes in glaucoma model tissues, such as the rodent optic nerve head

Diana C. Lozano, Dongseok Choi, Hari Jayaram, John Morrison, Elaine Johnson

Research output: Chapter in Book/Report/Conference proceedingChapter

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.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages299-310
Number of pages12
Volume1695
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1695
ISSN (Print)1064-3745

Keywords

  • Central nervous system
  • Glaucoma
  • Optic nerve head
  • Retina
  • RNA-seq
  • Rodent

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Fingerprint Dive into the research topics of 'Utilizing RNA-seq to identify differentially expressed genes in glaucoma model tissues, such as the rodent optic nerve head'. Together they form a unique fingerprint.

  • Cite this

    Lozano, D. C., Choi, D., Jayaram, H., Morrison, J., & Johnson, E. (2018). Utilizing RNA-seq to identify differentially expressed genes in glaucoma model tissues, such as the rodent optic nerve head. In Methods in Molecular Biology (Vol. 1695, pp. 299-310). (Methods in Molecular Biology; Vol. 1695). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7407-8_20