The Human Cell Atlas
Aviv Regev,Aviv Regev,Aviv Regev,Sarah A. Teichmann,Sarah A. Teichmann,Sarah A. Teichmann,Eric S. Lander,Eric S. Lander,Eric S. Lander,Ido Amit,Christophe Benoist,Ewan Birney,Bernd Bodenmiller,Bernd Bodenmiller,Peter J. Campbell,Peter J. Campbell,Piero Carninci,Menna R. Clatworthy,Hans Clevers,Bart Deplancke,Ian Dunham,James Eberwine,Roland Eils,Roland Eils,Wolfgang Enard,Andrew Farmer,Lars Fugger,Berthold Göttgens,Nir Hacohen,Nir Hacohen,Muzlifah Haniffa,Martin Hemberg,Seung K. Kim,Paul Klenerman,Paul Klenerman,Arnold R. Kriegstein,Ed S. Lein,Sten Linnarsson,Emma Lundberg,Emma Lundberg,Joakim Lundeberg,Partha P. Majumder,John C. Marioni,John C. Marioni,John C. Marioni,Miriam Merad,Musa M. Mhlanga,Martijn C. Nawijn,Mihai G. Netea,Garry P. Nolan,Dana Pe'er,Anthony Phillipakis,Chris P. Ponting,Stephen R. Quake,Wolf Reik,Wolf Reik,Wolf Reik,Orit Rozenblatt-Rosen,Joshua R. Sanes,Rahul Satija,Ton N. Schumacher,Alex K. Shalek,Alex K. Shalek,Alex K. Shalek,Ehud Shapiro,Padmanee Sharma,Jay W. Shin,Oliver Stegle,Michael R. Stratton,Michael J. T. Stubbington,Fabian J. Theis,Matthias Uhlen,Matthias Uhlen,Alexander van Oudenaarden,Allon Wagner,Fiona M. Watt,Jonathan S. Weissman,Barbara J. Wold,Ramnik J. Xavier,Nir Yosef,Nir Yosef,Human Cell Atlas Meeting Participants +81 more
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TLDR
An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease.Abstract:
The recent advent of methods for high-throughput single-cell molecular profiling has catalyzed a growing sense in the scientific community that the time is ripe to complete the 150-year-old effort to identify all cell types in the human body. The Human Cell Atlas Project is an international collaborative effort that aims to define all human cell types in terms of distinctive molecular profiles (such as gene expression profiles) and to connect this information with classical cellular descriptions (such as location and morphology). An open comprehensive reference map of the molecular state of cells in healthy human tissues would propel the systematic study of physiological states, developmental trajectories, regulatory circuitry and interactions of cells, and also provide a framework for understanding cellular dysregulation in human disease. Here we describe the idea, its potential utility, early proofs-of-concept, and some design considerations for the Human Cell Atlas, including a commitment to open data, code, and community.read more
Citations
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Journal ArticleDOI
Comprehensive Integration of Single-Cell Data.
Tim Stuart,Andrew Butler,Paul J. Hoffman,Christoph Hafemeister,Efthymia Papalexi,William M. Mauck,Yuhan Hao,Marlon Stoeckius,Peter Smibert,Rahul Satija +9 more
TL;DR: A strategy to "anchor" diverse datasets together, enabling us to integrate single-cell measurements not only across scRNA-seq technologies, but also across different modalities.
Journal ArticleDOI
Integrating single-cell transcriptomic data across different conditions, technologies, and species.
TL;DR: An analytical strategy for integrating scRNA-seq data sets based on common sources of variation is introduced, enabling the identification of shared populations across data sets and downstream comparative analysis.
Journal ArticleDOI
SCANPY: large-scale single-cell gene expression data analysis
TL;DR: This work presents Scanpy, a scalable toolkit for analyzing single-cell gene expression data that includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing, and simulation of gene regulatory networks, and AnnData, a generic class for handling annotated data matrices.
Journal ArticleDOI
Fast, sensitive and accurate integration of single-cell data with Harmony.
Ilya Korsunsky,Nghia Millard,Jean Fan,Kamil Slowikowski,Fan Zhang,Kevin Wei,Yuriy Baglaenko,Michael B. Brenner,Po-Ru Loh,Po-Ru Loh,Po-Ru Loh,Soumya Raychaudhuri +11 more
TL;DR: Harmony, for the integration of single-cell transcriptomic data, identifies broad and fine-grained populations, scales to large datasets, and can integrate sequencing- and imaging-based data.
Journal ArticleDOI
SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar,Carmen Bravo González-Blas,Thomas Moerman,Vân Anh Huynh-Thu,Hana Imrichova,Gert Hulselmans,Florian Rambow,Jean-Christophe Marine,Pierre Geurts,Jan Aerts,Joost van den Oord,Zeynep Kalender Atak,Jasper Wouters,Stein Aerts +13 more
TL;DR: On a compendium of single-cell data from tumors and brain, it is demonstrated that cis-regulatory analysis can be exploited to guide the identification of transcription factors and cell states.
References
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Journal ArticleDOI
Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens
Atray Dixit,Atray Dixit,Oren Parnas,Biyu Li,Jenny Chen,Jenny Chen,Charles P. Fulco,Charles P. Fulco,Livnat Jerby-Arnon,Nemanja D. Marjanovic,Nemanja D. Marjanovic,Danielle Dionne,Tyler Burks,Raktima Raychowdhury,Britt Adamson,Thomas M. Norman,Eric S. Lander,Eric S. Lander,Eric S. Lander,Jonathan S. Weissman,Jonathan S. Weissman,Nir Friedman,Nir Friedman,Aviv Regev,Aviv Regev,Aviv Regev +25 more
TL;DR: Perturb-seq as discussed by the authors combines single-cell RNA sequencing and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool.
Journal ArticleDOI
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
Darren A. Cusanovich,Riza M. Daza,Andrew Adey,Hannah A. Pliner,Lena Christiansen,Kevin L. Gunderson,Frank J. Steemers,Cole Trapnell,Jay Shendure +8 more
TL;DR: Combinatorial cellular indexing, a strategy for multiplex barcoding of thousands of single cells per experiment, was successfully used to investigate the genome-wide chromatin accessibility landscape in each of over 15,000 single cells, avoiding the need for compartmentalization of individual cells.
Journal ArticleDOI
Optical imaging. Expansion microscopy.
TL;DR: A new approach to image fixed biological samples by expanding the specimen under study reveals mouse brain substructures, and this process can be used to perform scalable superresolution microscopy with diffraction-limited microscopes.
Journal ArticleDOI
Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Karthik Shekhar,Sylvain W. Lapan,Sylvain W. Lapan,Irene E. Whitney,Nicholas M. Tran,Evan Z. Macosko,Evan Z. Macosko,Monika S. Kowalczyk,Xian Adiconis,Joshua Z. Levin,James Nemesh,James Nemesh,Melissa Goldman,Melissa Goldman,Steven A. McCarroll,Steven A. McCarroll,Constance L. Cepko,Constance L. Cepko,Aviv Regev,Aviv Regev,Aviv Regev,Joshua R. Sanes +21 more
TL;DR: This work provides a systematic methodology for achieving comprehensive molecular classification of neurons, identifies novel neuronal types, and uncovers transcriptional differences that distinguish types within a class.
Journal ArticleDOI
A small step for the cell, a giant leap for mankind: a hypothesis of neocortical expansion during evolution
TL;DR: Mutation of a regulatory gene(s) that controls the timing and ratio of symmetric and asymmetric modes of cell divisions in the proliferative zone could create an expanded cortical plate with enhanced capacity for establishing new patterns of connectivity that are validated through natural selection.
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