195 studies
5,000,851 cells
A single-cell survey of the small intestinal epitheliumAdam L. Haber, Moshe Biton, Noga Rogel, Rebecca H. Herbst, Karthik Shekhar, Christopher Smillie, Grace Burgin, Toni M. Delory, Michael R. Howitt, Yarden Katz, Itay Tirosh, Semir Beyaz, Danielle Dionne, Mei Zhang, Raktima Raychowdhury, Wendy S. Garrett, Orit Rozenblatt-Rosen, Hai Ning Shi, Omer Yilmaz, Ramnik J Xavier and Aviv Regev.     Nature 16 November 2017 DOI: 10.1038/nature24489Contact: aregev@broadinstitute.orgSummaryIntestinal epithelial cells absorb nutrients, respond to microbes, function as a barrier and help to coordinate immune responses. Here we report profiling of 53,193 individual epithelial cells from the small intestine and organoids of mice, which enabled the identification and characterization... (continued)
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.aad7038Contact: naomi@broadinstitute.orgSingle 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 to profile... (continued)
  Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors Alexandra-Chloé Villani, Rahul Satija, Gary Reynolds, Siranush Sarkizova, Karthik Shekhar, James Fletcher, Morgane Griesbeck, Andrew Butler, Shiwei Zheng, Suzan Lazo, Laura Jardine, David Dixon, Emily Stephenson, Emil Nilsson, Ida Grundberg, David McDonald, Andrew Filby, Weibo Li, Philip L. De Jager, Orit Rozenblatt-Rosen, Andrew A. Lane, Muzlifah Haniffa, Aviv Regev, Nir Hacohen Science 21 April 2017 DOI: 10.1126/science.aah4573 Contact: cvillani@broadinstitute.org   SUMMARY Introduction Dendritic cells (DCs) and monocytes consist of multiple specialized subtypes that play a central role in pathogen sensing, phagocytosis, and antigen presentation. However, their identities and interrelationships... (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)
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)

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