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<p>Affymetrix Mouse Gene 2.0 ST Array: These expression arrays have been designed with a median of 22 unique probes per transcript. Each unique probe is 25 bases in length, which means that the array measures a median of 550 bases per transcript. The arrays provide comprehensive transcriptome coverage with over 30,000 coding and non-coding transcripts. In addition there is coverage for over 600 microRNAs. For some arrays the RNA was pooled from two retinas and for other arrays were run on a single retina. Dr. XiangDi Wang (UTHSC) and Becky King (Emory) were involved in the retinal extractions and isolation of RNA. The Affymetrix arrays were run by two different research cores: the Molecular Resource Center at UTHSC (Dr. William Taylor Director) and the Integrated Genomics Core at Emory University by Robert B Isett (Dr. Michael E. Zwick, Director). In a separate set of experiments we tested a set of arrays from C57BL/6J retinas run at each facility to determine if there were batch effects or other confounding differences in the results. We could not detect any significant difference in the arrays run at UTHSC or at Emory University. Thus, we have included both sets of data into the analysis.</p>
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