@article {1363276,
	title = {Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes},
	journal = {BMC Genomics},
	volume = {14},
	year = {2013},
	month = {2013 Jul 18},
	pages = {486},
	abstract = {BACKGROUND: The retina is a complex tissue comprised of multiple cell types that is affected by a diverse set of diseases that are important causes of vision loss. Characterizing the transcripts, both annotated and novel, that are expressed in a given tissue has become vital for understanding the mechanisms underlying the pathology of disease. RESULTS: We sequenced RNA prepared from three normal human retinas and characterized the retinal transcriptome at an unprecedented level due to the increased depth of sampling provided by the RNA-seq approach. We used a non-redundant reference transcriptome from all of the empirically-determined human reference tracks to identify annotated and novel sequences expressed in the retina. We detected 79,915 novel alternative splicing events, including 29,887 novel exons, 21,757 3{\textquoteright} and 5{\textquoteright} alternate splice sites, and 28,271 exon skipping events. We also identified 116 potential novel genes. These data represent a significant addition to the annotated human transcriptome. For example, the novel exons detected increase the number of identified exons by 3\%. Using a high-throughput RNA capture approach to validate 14,696 of these novel transcriptome features we found that 99\% of the putative novel events can be reproducibly detected. Further, 15-36\% of the novel splicing events maintain an open reading frame, suggesting they produce novel protein products. CONCLUSIONS: To our knowledge, this is the first application of RNA capture to perform large-scale validation of novel transcriptome features. In total, these analyses provide extensive detail about a previously uncharacterized level of transcript diversity in the human retina.},
	keywords = {Adult, Alternative Splicing, Computational Biology, DNA-Binding Proteins, Female, Gene Expression Profiling, Gene Expression Regulation, Genetic Association Studies, High-Throughput Nucleotide Sequencing, Humans, Male, Middle Aged, Molecular Sequence Annotation, Neoplasm Proteins, Organ Specificity, Reproducibility of Results, Retina, RNA Isoforms, Transcriptome},
	issn = {1471-2164},
	doi = {10.1186/1471-2164-14-486},
	author = {Farkas, Michael H and Grant, Gregory R and White, Joseph A and Sousa, Maria E and Consugar, Mark B and Pierce, Eric A}
}
