Development of a microarray chip for gene expression in rabbit ocular research

Michael P. Popp, Li Liu, Adrian Timmers, Douglas W. Esson, Lineu Shiroma, Craig Meyers, Scott Berceli, Ming Tao, Graeme Wistow, Gregory S. Schultz, Mark B. Sherwood

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Purpose: To develop a microarray for the rabbit that can be used for ocular gene expression research. Methods: Messenger RNA was isolated from anterior segment tissues (cornea, conjunctiva, and iris) and posterior segment tissues (lens, retina, and sclera) of rabbit eyes and used to create two independent cDNA libraries through the NEIBank project. Clones from each of these libraries were sequenced from both the 5′ and 3′ ends. These sequences and those from the National Center for Biotechnology Information (NCBI) taxonomy database for rabbit were combined and electronically assembled into a set of unique nonoverlapping continuous sequences (contigs). For each contig, a homology search was performed using BLASTX and BLASTN against both the NCBI NR and NT databases to provide gene annotation. Unique contigs were sent to Agilent Technologies, where 60 base oligonucleotide probes were designed and synthesized, in situ, on two different arrays in an 8 array × 1900 element format. Glaucoma filtration surgery was performed on one eye of six rabbits. After 14 days, tissue was harvested from the conjunctiva and Tenon's capsule of both the surgically treated and untreated control eyes. Total RNA from each sample was labeled with cyanine dyes and hybridized to our custom microarrays. Results: Of the 3,154 total probes present on the two arrays, 2,522 had a signal value above the background. The expression of 315 genes was significantly altered by glaucoma filtration surgery. Genes whose expression was altered included proteins associated with inflammatory response, defense response, and proteins involved in synthesis of the extracellular matrix. Conclusions: The results of this rabbit microarray study are consistent with those from other wound healing studies, indicating that this array can provide valid information on broad patterns of gene expression. This is the first microarray available for rabbit studies and is a valuable tool that can be used to study molecular events in the eye.

Original languageEnglish (US)
Pages (from-to)164-173
Number of pages10
JournalMolecular Vision
Volume13
StatePublished - 2007
Externally publishedYes

Fingerprint

Rabbits
Gene Expression
Research
Filtering Surgery
Information Centers
Conjunctiva
Biotechnology
Glaucoma
Tenon Capsule
Databases
Molecular Sequence Annotation
Sclera
Oligonucleotide Probes
Iris
Gene Library
Wound Healing
Cornea
Lenses
Libraries
Extracellular Matrix

ASJC Scopus subject areas

  • Ophthalmology

Cite this

Popp, M. P., Liu, L., Timmers, A., Esson, D. W., Shiroma, L., Meyers, C., ... Sherwood, M. B. (2007). Development of a microarray chip for gene expression in rabbit ocular research. Molecular Vision, 13, 164-173.

Development of a microarray chip for gene expression in rabbit ocular research. / Popp, Michael P.; Liu, Li; Timmers, Adrian; Esson, Douglas W.; Shiroma, Lineu; Meyers, Craig; Berceli, Scott; Tao, Ming; Wistow, Graeme; Schultz, Gregory S.; Sherwood, Mark B.

In: Molecular Vision, Vol. 13, 2007, p. 164-173.

Research output: Contribution to journalArticle

Popp, MP, Liu, L, Timmers, A, Esson, DW, Shiroma, L, Meyers, C, Berceli, S, Tao, M, Wistow, G, Schultz, GS & Sherwood, MB 2007, 'Development of a microarray chip for gene expression in rabbit ocular research', Molecular Vision, vol. 13, pp. 164-173.
Popp MP, Liu L, Timmers A, Esson DW, Shiroma L, Meyers C et al. Development of a microarray chip for gene expression in rabbit ocular research. Molecular Vision. 2007;13:164-173.
Popp, Michael P. ; Liu, Li ; Timmers, Adrian ; Esson, Douglas W. ; Shiroma, Lineu ; Meyers, Craig ; Berceli, Scott ; Tao, Ming ; Wistow, Graeme ; Schultz, Gregory S. ; Sherwood, Mark B. / Development of a microarray chip for gene expression in rabbit ocular research. In: Molecular Vision. 2007 ; Vol. 13. pp. 164-173.
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