Serial analysis of gene expression (SAGE) in normal human trabecular meshwork

Yutao Liu, Drew Munro, David Layfield, Andrew Dellinger, Jeffrey Walter, Katherine Peterson, Catherine Bowes Rickman, R. Rand Allingham, Michael A. Hauser

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD Purpose: To identify the genes expressed in normal human trabecular meshwork tissue, a tissue e critical to the pathogenesis of glaucoma. Methods: Total RNA was extracted from human trabecular meshwork (HTM) harvested from 3 different donors. Extracted RNA was used to synthesize individual SAGE (serial analysis of gene expression) libraries using the I-SAGE Long kit from Invitrogen. Libraries were analyzed using SAGE 2000 software to extract the 17 base pair sequence tags. The extracted sequence tags were mapped to the genome using SAGE Genie map. Results: A total of 298,834 SAGE tags were identified from all HTM libraries (96,842, 88,126, and 113,866 tags, respectively). Collectively, there were 107,325 unique tags. There were 10,329 unique tags with a minimum of 2 counts from a single library. These tags were mapped to known unique Unigene clusters. Approximately 29% of the tags (orphan tags) did not map to a known Unigene cluster. Thirteen percent of the tags mapped to at least 2 Unigene clusters. Sequence tags from many glaucoma-related genes, including myocilin, optineurin, and WD repeat domain 36, were identified. Conclusions: This is the first time SAGE analysis has been used to characterize the gene expression profile in normal HTM. SAGE analysis provides an unbiased sampling of gene expression of the target tissue. These data will provide new and valuable information to improve understanding of the biology of human aqueous outflow.

Original languageEnglish (US)
Pages (from-to)885-893
Number of pages9
JournalMolecular Vision
Volume17
StatePublished - Jan 1 2011

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Trabecular Meshwork
Gene Expression
Libraries
Glaucoma
National Eye Institute (U.S.)
RNA
Orphaned Children
National Institutes of Health (U.S.)
Genomics
Molecular Structure
Gene Library
Transcriptome
Base Pairing
Genes
Software
Tissue Donors
Genome

ASJC Scopus subject areas

  • Ophthalmology

Cite this

Liu, Y., Munro, D., Layfield, D., Dellinger, A., Walter, J., Peterson, K., ... Hauser, M. A. (2011). Serial analysis of gene expression (SAGE) in normal human trabecular meshwork. Molecular Vision, 17, 885-893.

Serial analysis of gene expression (SAGE) in normal human trabecular meshwork. / Liu, Yutao; Munro, Drew; Layfield, David; Dellinger, Andrew; Walter, Jeffrey; Peterson, Katherine; Rickman, Catherine Bowes; Rand Allingham, R.; Hauser, Michael A.

In: Molecular Vision, Vol. 17, 01.01.2011, p. 885-893.

Research output: Contribution to journalArticle

Liu, Y, Munro, D, Layfield, D, Dellinger, A, Walter, J, Peterson, K, Rickman, CB, Rand Allingham, R & Hauser, MA 2011, 'Serial analysis of gene expression (SAGE) in normal human trabecular meshwork', Molecular Vision, vol. 17, pp. 885-893.
Liu Y, Munro D, Layfield D, Dellinger A, Walter J, Peterson K et al. Serial analysis of gene expression (SAGE) in normal human trabecular meshwork. Molecular Vision. 2011 Jan 1;17:885-893.
Liu, Yutao ; Munro, Drew ; Layfield, David ; Dellinger, Andrew ; Walter, Jeffrey ; Peterson, Katherine ; Rickman, Catherine Bowes ; Rand Allingham, R. ; Hauser, Michael A. / Serial analysis of gene expression (SAGE) in normal human trabecular meshwork. In: Molecular Vision. 2011 ; Vol. 17. pp. 885-893.
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