The regional molecular distinction is greatest between macula and periphery and decreases between different peripheral regions within a tissue.
The MAK gene was expressed at lower levels in macula than in extramacular regions, but did not exhibit a significant difference between nasal and temporal retina. Consistent with previous studies, BEST1 expression was lower in macular than extramacular regions. Within the RPE/choroid, RPE-specific genes were upregulated at the periphery while endothelium associated genes were upregulated in the macula. Photoreceptor-specific genes were enriched in the peripheral samples, while ganglion cell and amacrine cell genes were enriched in the macula. Numerous transcription factors were differentially expressed between regions of the retina and RPE/choroid. Retina and RPE/choroid samples were clearly distinguishable at the transcriptome level.
#CUFFLINKS HIDATA SOFTWARE#
Digital read files were mapped to the human genome and analyzed for differential expression using the Tuxedo software suite. RNA from temporal, macular, and nasal retina and RPE/choroid from four human donor eyes was extracted, poly-A selected, fragmented, and sequenced as 100 bp read pairs. To investigate regional difference in molecular composition of ocular tissues, we assessed differential gene expression across the temporal, macular, and nasal retina and retinal pigment epithelium (RPE)/choroid of human eyes using RNA-Seq. While much is known about the distribution of cell types in the retina, the distribution of molecular components across the posterior pole of the eye has not been well-studied. Many retinal diseases, such as Best disease and male germ cell associated kinase ( MAK)-associated retinitis pigmentosa, preferentially affect distinct topographic regions of the retina. CUFFLINKS 4 ME (UK) LIMITED, 1e Ferozeshah Road, Northfields, Devizes. LOWDATA (too complex or shallowly sequenced), HIDATA (too many fragments in locus), or FAIL. UJ HIDATA INGATLAN LTD, INTERNATIONAL HOUSE 124 CROMWELL ROAD, KENSIGTON. Each draw is a number of fragments that will be probabilistically assigned to the transcripts in the transcriptome.
Default: 1000000 max-frag-count-drawsProper spatial differentiation of retinal cell types is necessary for normal human vision. Cufflinks for identifying differentially expressed genes. Skipped loci are marked with status HIDATA.
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