title: Microarray analysis of gene expression in human donor sclera.
abstract: OBJECTIVE
  To develop gene expression profiles of human sclera to allow for the identification of novel, uncharacterized genes in this tissue-type, and to identify candidate genes for scleral disorders.
  
  
  METHODS
  Total RNA was isolated from 6 donor sources of human sclerae, and reverse transcribed into cDNA using a T7-(dT) 24 primer. The resulting cDNA was in vitro transcribed to produce biotin-labeled cRNA, fragmented, and mixed with hybridization controls before a 16 h hybridization step with oligonucleotide probes on 6 Affymetrix U95A chips. The chips were scanned twice at 570 nM and the data collected using GeneChip software. Array analyses were carried out with Microarray Suite, version 5.0 (Affymetrix), using the expression analysis algorithm to run an absolute analysis after cell intensities were computed. All arrays were scaled to the same target intensity using all probe sets. Reverse-transcription polymerase chain reaction (RT-PCR) was performed to validate the microarray results.
  
  
  RESULTS
  There were 3,751 genes with "present" calls assigned independently to all six human scleral samples. These genes could be clustered into 4 major categories; transcription (10%), metabolism (8.8%), cell growth and proliferation (5.4%), and extracellular matrix (2%). Many extracellular matrix proteins, such as collagens 6A3 and 10A1, thrombospondins 2 and 4, and dystroglycan have not previously been shown to be expressed in sclera. RT-PCR results confirmed scleral expression in 7 extracellular matrix genes examined.
  
  
  CONCLUSIONS
  This study demonstrated the utility of gene microarray technology in identifying global patterns of scleral gene expression, and provides an extended list of genes expressed in human sclera. Identification of genes expressed in sclera contributes to our understanding of scleral biology, and potentially provides positional candidate genes for scleral disorders such as high myopia.
authors.affiliation: Division of Ophthalmology, Children's Hospital of Philadelphia and the University of Pennsylvania, Philadelphia, PA 19104, USA. youngt@email.chop.edu
authors.forename: Terri L
authors.initials: TL
authors.lastname: Young
authors.forename: Genaro S
authors.initials: GS
authors.lastname: Scavello
authors.forename: Prasuna C
authors.initials: PC
authors.lastname: Paluru
authors.forename: Jonathan D
authors.initials: JD
authors.lastname: Choi
authors.forename: Eric F
authors.initials: EF
authors.lastname: Rappaport
authors.forename: Jody A
authors.initials: JA
authors.lastname: Rada
mesh_terms: D000328:Adult; D000368:Aged; D016326:Extracellular Matrix Proteins / Q000235:genetics; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D008297:Male; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D012313:RNA / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012590:Sclera / Q000378:metabolism*; D014019:Tissue Donors
chemical_list: D016326:Extracellular Matrix Proteins; D015345:Oligonucleotide Probes; D012313:RNA