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
Deciphering Cell Fate Decision by Integrated Single-Cell Sequencing Analysis.
Sagar,Dominic Grün,Dominic Grün +2 more
TL;DR: How the computational tools available to reconstruct lineage trajectories, quantify cell fate bias, and perform dimensionality re- duction for data visualization are providing new mechanistic insights into the process of cell fate decision is discussed.
Journal ArticleDOI
Expansion microscopy: enabling single cell analysis in intact biological systems
TL;DR: Expansion microscopy is a technology that physically magnifies tissues in an isotropic way, thereby achieving super‐resolution microscopy on diffraction‐limited microscopes, enabling rapid image acquisition and large field of view.
Posted ContentDOI
Wiring together large single-cell RNA-seq sample collections
Nikolaos Barkas,Petukhov,Petukhov,Nikolaeva D,Lozinsky Y,Samuel Demharter,Konstantin Khodosevich,Peter V. Kharchenko +7 more
TL;DR: A flexible approach, called Conos (Clustering On Network Of Samples), that relies on multiple plausible inter-sample mappings to construct a global graph connecting all measured cells, which enables investigators to balance between resolution and breadth of the detected subpopulations.
Journal ArticleDOI
TSEA-DB: a trait-tissue association map for human complex traits and diseases.
TL;DR: A reference database for trait-associated tissue specificity based on genome-wide association study (GWAS) results, named Tissue-Specific Enrichment Analysis DataBase (TSEA-DB), which aims to provide reference tissue(s) enriched with the genes from GWAS.
Journal ArticleDOI
Probe-Seq enables transcriptional profiling of specific cell types from heterogeneous tissue by RNA-based isolation.
Ryoji Amamoto,Mauricio D. Garcia,Emma R. West,Jiho Choi,Sylvain W. Lapan,Elizabeth A. Lane,Norbert Perrimon,Constance L. Cepko +7 more
TL;DR: Probe-Seq is developed, which allows deep transcriptional profiling of specific cell types isolated using RNA as the defining feature, and is compatible with frozen nuclei, making cell types within archival tissue immediately accessible.
References
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TL;DR: The derivation of a number of tissue culture cell lines which secrete anti-sheep red blood cell (SRBC) antibodies is described here, made by fusion of a mouse myeloma and mouse spleen cells from an immunised donor.
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Fast unfolding of communities in large networks
Vincent D. Blondel,Jean-Loup Guillaume,Jean-Loup Guillaume,Renaud Lambiotte,Renaud Lambiotte,Etienne Lefebvre +5 more
TL;DR: This work proposes a heuristic method that is shown to outperform all other known community detection methods in terms of computation time and the quality of the communities detected is very good, as measured by the so-called modularity.
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Journal ArticleDOI
Fast unfolding of communities in large networks
Vincent D. Blondel,Jean-Loup Guillaume,Jean-Loup Guillaume,Renaud Lambiotte,Renaud Lambiotte,Etienne Lefebvre +5 more
TL;DR: In this paper, the authors proposed a simple method to extract the community structure of large networks based on modularity optimization, which is shown to outperform all other known community detection methods in terms of computation time.
Journal ArticleDOI
Tissue-based map of the human proteome
Mathias Uhlén,Mathias Uhlén,Linn Fagerberg,Björn M. Hallström,Cecilia Lindskog,Per Oksvold,Adil Mardinoglu,Åsa Sivertsson,Caroline Kampf,Evelina Sjöstedt,Evelina Sjöstedt,Anna Asplund,IngMarie Olsson,Karolina Edlund,Emma Lundberg,Sanjay Navani,Cristina Al-Khalili Szigyarto,Jacob Odeberg,Dijana Djureinovic,Jenny Ottosson Takanen,Sophia Hober,Tove Alm,Per-Henrik Edqvist,Holger Berling,Hanna Tegel,Jan Mulder,Johan Rockberg,Peter Nilsson,Jochen M. Schwenk,Marica Hamsten,Kalle von Feilitzen,Mattias Forsberg,Lukas Persson,Fredric Johansson,Martin Zwahlen,Gunnar von Heijne,Jens Nielsen,Jens Nielsen,Fredrik Pontén +38 more
TL;DR: In this paper, a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level.
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