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)
---------------------------   -------------------   -------------------   -------------------   -----------   ------------
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
Confirmatory Real-time PCR    not neccesary         yes                   not necessary         RT PCR only   yes
Bioinformatics                SAGE2000              SAM                   SAGE2000/EYESAGE      Q-gene        Rosetta
Initial confirmation by IHC   no                    no                    no                    no            yes

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