title: Development of a microarray chip for gene expression in rabbit ocular research.
abstract: OBJECTIVE
  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 x 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.
authors.affiliation: University of Florida's Interdisciplinary Center for Biotechnology Research, University of Florida, Gainsville, FL 32610-0294, USA. mpopp@obgyn.ufl.edu <mpopp@obgyn.ufl.edu>
authors.forename: Michael P
authors.initials: MP
authors.lastname: Popp
authors.forename: Li
authors.initials: L
authors.lastname: Liu
authors.forename: Adrian
authors.initials: A
authors.lastname: Timmers
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Esson
authors.forename: Lineu
authors.initials: L
authors.lastname: Shiroma
authors.forename: Craig
authors.initials: C
authors.lastname: Meyers
authors.forename: Scott
authors.initials: S
authors.lastname: Berceli
authors.forename: Ming
authors.initials: M
authors.lastname: Tao
authors.forename: Graeme
authors.initials: G
authors.lastname: Wistow
authors.forename: Gregory S
authors.initials: GS
authors.lastname: Schultz
authors.forename: Mark B
authors.initials: MB
authors.lastname: Sherwood
mesh_terms: D000818:Animals; D035843:Biomedical Research / Q000379:methods*; D003199:Computer Systems; D005123:Eye / Q000378:metabolism*; D018463:Filtering Surgery; D015870:Gene Expression; D015723:Gene Library; D005901:Glaucoma / Q000235:genetics / Q000378:metabolism / Q000601:surgery; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D011817:Rabbits / Q000235:genetics*