Single Cell Portal BETA

Visualization portal for single cell RNA-seq data.

Now featuring 43 studies with 496,366 cells.

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Single nucleus RNA-seq of cell diversity in the adult mouse hippocampus. Habib N, Li Y, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta J, Hession C, Zhang F, Regev A. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Science  28 Jul 2016 DOI: 10.1126/science.aad7038 Contact: naomi@broadinstitute.org Single cell RNA-Seq provides rich information about cell types and states. However, it is difficult to capture rare dynamic processes, such as adult neurogenesis, because isolation of rare neurons from adult tissue is challenging and markers for each phase are limited. Here, we develop Div-Seq, which combines scalable single-nucleus RNA-Seq (sNuc-Seq) with pulse labeling of proliferating cells by EdU... (continued)
Retinal Bipolar Neuron Drop-Seq Karthik Shekhar, Sylvain W. Lapan, Irene E. Whitney, Nicholas M. Tran, Evan Z. Macosko, Monika Kowalczyk, Xian Adiconis, Joshua Z. Levin, James Nemesh, Melissa Goldman, Steven A. McCarroll, Constance L. Cepko, Aviv Regev, Joshua R. Sanes. Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics. Cell. Volume 166, Issue 5, p1308–1323.e30, 25 August 2016. DOI: http://dx.doi.org/10.1016/j.cell.2016.07.054 Contact: Karthik Shekhar at karthik@broadinstitute.org   Patterns of gene expression can be used to characterize and classify neuronal types. It is challenging, however, to generate taxonomies that fulfill the essential criteria of being comprehensive, harmonizing with conventional classification schemes, and lacking superfluous subdivisions of genuine types. To address these challenges, we used massively parallel single-cell RNA profiling and optimized computational methods on a heterogeneous class of... (continued)
Citation: Campbell JN, Macosko EZ, Fenselau H, Pers TH, Lyubetskaya A, Tenen D, Goldman M, Verstegen AM, Resch JM, McCarroll SA, Rosen ED, Lowell BB, Tsai LT, A molecular census of arcuate hypothalamus and median eminence cell types. Nature Neuroscience. 06 February 2017; 20(3): 484–496 PMID: 28166221 Contact: Linus Tsai (ltsai@bidmc.harvard.edu) GEO: GSE93374 Abstract: The hypothalamic arcuate–median eminence complex (Arc-ME) controls energy balance, fertility and growth through molecularly distinct cell types, many of which remain unknown. To catalog cell types in an unbiased way, we profiled gene expression in 20,921 individual cells in and around the adult mouse Arc-ME using Drop-seq. We... (continued)
Single-cell RNA-seq from 1,301 cells in the anterior lateral motor cortex (ALM), a sub-region of the premotor cortex. All cells were collected from 56±3 day-old adult male mice. Further details and a tecnical whitepaper can be found on the Allen Institute for Brain Science RNA-seq Transcriptomic Profiling page: http://celltypes.brain-map.org/rnaseq