Brain circuits are assembled from a large variety of morphologically and functionally diverse cell types. It is not known how the intermingled cell types of an individual adult brain region differ in their expressed genomes. Here we describe an atlas of cell type transcriptomes in one brain region, the mouse retina. We found that each adult cell type expressed a specific set of genes, including a unique set of transcription factors, forming a 'barcode' for cell identity. Cell type transcriptomes carried enough information to categorize cells into morphological classes and types. Several genes that were specifically expressed in particular retinal circuit elements, such as inhibitory neuron types, are associated with eye diseases. The resource described here allows gene expression to be compared across adult retinal cell types, experimenting with specific transcription factors to differentiate stem or somatic cells to retinal cell types, and predicting cellular targets of newly discovered disease-associated genes.
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We thank S. Djaffer, J. Jüttner, J. Hall and Y. Shimada for technical assistance, E. Oakeley for comments on the experimental design, D. Balya for providing help with programming, and K. Farrow, S. Rompani, K. Yonehara, V. Busskamp, S. Oakeley, P. King, A. Matus, S. Arber and F. Rijli for comments on the manuscript. We thank Z. Raics for making the webpage, and L. Kus and S. Gong (Rockefeller University) for help and for BACs from the GENSAT project. We thank I. Provencio (University of Virginia) for providing the melanopsin antibody. The study was supported by Friedrich Miescher Institute funds, Alcon award, a National Center of Competence in Research Genetics grant, a European Research Council grant, a Swiss-Hungarian grant, and RETICIRC, TREATRUSH, SEEBETTER and OPTONEURO grants from the European Union to B.R.
The authors declare no competing financial interests.
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Siegert, S., Cabuy, E., Scherf, B. et al. Transcriptional code and disease map for adult retinal cell types. Nat Neurosci 15, 487–495 (2012). https://doi.org/10.1038/nn.3032
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