Table 6 of
Soest, Mol Vis 2007;
13:1608-1617.Table 6 of
Soest, Mol Vis 2007;
13:1608-1617.
Table 6. Relative strength and weaknesses of retinal pigment epithelium gene expression studies, with overlapping research questions
Shown in the table are steps followed in gene expression studies on human donor eyes. LDM represents laser dissection microscopy; SAGE represents a technique called serial analysis of gene expression; 4K refers to 4000 genes. P32 refers to the radioactive labeling technique used for the array studies. Filter arrays refers to nylon membrane on which cDNA clones are spotted. 22 K refers to 22000 gene entries used. Oligo arrays are small glass plates on which synthetic oligonucleotide strands were synthesized. RT-PCR represents real time polymerase chain reaction. SAGE2000, SAM, EYESAGE, Q-gene, Rosetta Resolver are names of computer program packages designed for use the studies mentioned. IHC represents immunohistochemistry.
van Soest
Methods (used) Sharon [17] Ishabisha [8] Bowes Rickman [18] Koicok [20] (this study)
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Patient/donor selection extraocular disease selected extraocular disease selected selected
Postmortem times short long short average average
General evaluation yes yes yes yes yes
Histological evaluation no yes no no yes
Harvesting RPE cells mechanical LDM mechanical mechanical? LDM
Contamination RPE cells RPE/choroid little RPE/choroid RPE/choroid little
RNA isolation/quality check good good good good good
Method/Microarrays used SAGE 4K P32 filter array SAGE Not done 22K oligo
arrays
Confirmatory Real-time PCR not neccesary yes not necessary RT PCR only yes
Bioinformatics SAGE2000 SAM SAGE2000/EYESAGE Q-gene Rosetta
Resolver
Initial confirmation by IHC no no no no yes
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