High-definition spatial transcriptomics for in situ tissue profiling.
Sanja Vickovic,Sanja Vickovic,Gökcen Eraslan,Fredrik Salmén,Johanna Klughammer,Linnea Stenbeck,Denis Schapiro,Denis Schapiro,Tarmo Äijö,Richard Bonneau,Ludvig Bergenstråhle,José Fernández Navarro,Joshua Gould,Gabriel K. Griffin,Gabriel K. Griffin,Åke Borg,Mostafa Ronaghi,Jonas Frisén,Joakim Lundeberg,Joakim Lundeberg,Aviv Regev,Aviv Regev,Patrik L. Ståhl +22 more
TLDR
High-definition spatial transcriptomics is developed, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array, which opens the way to high-resolution spatial analysis of cells and tissues.Abstract:
Spatial and molecular characteristics determine tissue function, yet high-resolution methods to capture both concurrently are lacking. Here, we developed high-definition spatial transcriptomics, which captures RNA from histological tissue sections on a dense, spatially barcoded bead array. Each experiment recovers several hundred thousand transcript-coupled spatial barcodes at 2-μm resolution, as demonstrated in mouse brain and primary breast cancer. This opens the way to high-resolution spatial analysis of cells and tissues.read more
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Integrated analysis of multimodal single-cell data
Yuhan Hao,Stephanie Hao,Erica Andersen-Nissen,William M. Mauck,Shiwei Zheng,Andrew Butler,Maddie Jane Lee,Aaron J. Wilk,Charlotte A. Darby,Michael Zager,Paul Hoffman,Marlon Stoeckius,Efthymia Papalexi,Eleni P. Mimitou,Jaison Jain,Avi Srivastava,Tim Stuart,Lamar M. Fleming,Bertrand Z. Yeung,Angela J. Rogers,Juliana M. McElrath,Catherine A. Blish,Raphael Gottardo,Peter Smibert,Rahul Satija +24 more
TL;DR: Weighted-nearest neighbor analysis as mentioned in this paper is an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities.
Posted ContentDOI
Integrated analysis of multimodal single-cell data
Yuhan Hao,Stephanie Hao,Erica Andersen-Nissen,William M. Mauck,Shiwei Zheng,Andrew Butler,Maddie Jane Lee,Aaron J. Wilk,Charlotte A. Darby,Michael Zagar,Paul Hoffman,Marlon Stoeckius,Efthymia Papalexi,Eleni P. Mimitou,Jaison Jain,Avi Srivastava,Tim Stuart,Lamar Ballweber Fleming,Bertrand Z. Yeung,Angela J. Rogers,Juliana M. McElrath,Catherine A. Blish,Raphael Gottardo,Peter Smibert,Rahul Satija +24 more
TL;DR: ‘weighted-nearest neighbor’ analysis is introduced, an unsupervised framework to learn the relative utility of each data type in each cell, enabling an integrative analysis of multiple modalities.
Journal ArticleDOI
NicheNet: modeling intercellular communication by linking ligands to target genes
TL;DR: NicheNet is presented, a method that predicts ligand–target links between interacting cells by combining their expression data with prior knowledge on signaling and gene regulatory networks, and can infer active ligands and their gene regulatory effects on interacting cells.
Journal ArticleDOI
Fibrosis: from mechanisms to medicines
TL;DR: The transformative experimental strategies that are being leveraged to dissect the key cellular and molecular mechanisms that regulate fibrosis, and the translational approaches that are enabling the emergence of precision medicine-based therapies for patients with fibrosis are discussed.
Journal ArticleDOI
Deciphering cell-cell interactions and communication from gene expression.
TL;DR: This Review highlights discoveries enabled by analyses of cell–cell interactions from transcriptomic data and reviews the methods and tools used in this context.
References
More filters
Journal ArticleDOI
Fiji: an open-source platform for biological-image analysis
Johannes Schindelin,Ignacio Arganda-Carreras,Erwin Frise,Verena Kaynig,Mark Longair,Tobias Pietzsch,Stephan Preibisch,Curtis Rueden,Stephan Saalfeld,Benjamin Schmid,Jean-Yves Tinevez,Daniel J. White,Volker Hartenstein,Kevin W. Eliceiri,Pavel Tomancak,Albert Cardona +15 more
TL;DR: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.
Journal ArticleDOI
STAR: ultrafast universal RNA-seq aligner
Alexander Dobin,Carrie A. Davis,Felix Schlesinger,Jorg Drenkow,Chris Zaleski,Sonali Jha,Philippe Batut,Mark Chaisson,Thomas R. Gingeras +8 more
TL;DR: The Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure outperforms other aligners by a factor of >50 in mapping speed.
Journal ArticleDOI
HTSeq—a Python framework to work with high-throughput sequencing data
TL;DR: This work presents HTSeq, a Python library to facilitate the rapid development of custom scripts for high-throughput sequencing data analysis, and presents htseq-count, a tool developed with HTSequ that preprocesses RNA-Seq data for differential expression analysis by counting the overlap of reads with genes.
Journal ArticleDOI
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Evan Z. Macosko,Evan Z. Macosko,Anindita Basu,Anindita Basu,Rahul Satija,Rahul Satija,James Nemesh,James Nemesh,Karthik Shekhar,Melissa Goldman,Melissa Goldman,Itay Tirosh,Allison R. Bialas,Nolan Kamitaki,Nolan Kamitaki,Emily M. Martersteck,John J. Trombetta,David A. Weitz,Joshua R. Sanes,Alex K. Shalek,Alex K. Shalek,Alex K. Shalek,Aviv Regev,Aviv Regev,Aviv Regev,Steven A. McCarroll,Steven A. McCarroll +26 more
TL;DR: Drop-seq will accelerate biological discovery by enabling routine transcriptional profiling at single-cell resolution by separating them into nanoliter-sized aqueous droplets, associating a different barcode with each cell's RNAs, and sequencing them all together.
Journal ArticleDOI
Genome-wide atlas of gene expression in the adult mouse brain
Ed S. Lein,Michael Hawrylycz,Nancy Ao,Mikael Ayres,Amy Bensinger,Amy Bernard,Andrew F. Boe,Mark S. Boguski,Mark S. Boguski,Kevin S. Brockway,Emi J. Byrnes,Lin Chen,Li Chen,Tsuey-Ming Chen,Mei Chi Chin,Jimmy Chong,Brian E. Crook,Aneta Czaplinska,Chinh Dang,Suvro Datta,Nick Dee,Aimee L. Desaki,Tsega Desta,Ellen Diep,Tim A. Dolbeare,Matthew J. Donelan,Hong-Wei Dong,Jennifer G. Dougherty,Ben J. Duncan,Amanda Ebbert,Gregor Eichele,Lili K. Estin,Casey Faber,Benjamin A.C. Facer,Rick Fields,Shanna R. Fischer,Tim P. Fliss,Cliff Frensley,Sabrina N. Gates,Katie J. Glattfelder,Kevin R. Halverson,Matthew R. Hart,John G. Hohmann,Maureen P. Howell,Darren P. Jeung,Rebecca A. Johnson,Patrick T. Karr,Reena Kawal,Jolene Kidney,Rachel H. Knapik,Chihchau L. Kuan,James H. Lake,Annabel R. Laramee,Kirk D. Larsen,Christopher Lau,Tracy Lemon,Agnes J. Liang,Ying Liu,Lon T. Luong,Jesse Michaels,Judith J. Morgan,Rebecca J. Morgan,Marty Mortrud,Nerick Mosqueda,Lydia Ng,Randy Ng,Geralyn J. Orta,Caroline C. Overly,Tu H. Pak,Sheana Parry,Sayan Dev Pathak,Owen C. Pearson,Ralph B. Puchalski,Zackery L. Riley,Hannah R. Rockett,Stephen A. Rowland,Joshua J. Royall,Marcos J. Ruiz,Nadia R. Sarno,Katherine Schaffnit,Nadiya V. Shapovalova,Taz Sivisay,Clifford R. Slaughterbeck,Simon Smith,Kimberly A. Smith,Bryan I. Smith,Andy J. Sodt,Nick N. Stewart,Kenda-Ruth Stumpf,Susan M. Sunkin,Madhavi Sutram,Angelene Tam,Carey D. Teemer,Christina Thaller,Carol L. Thompson,Lee R. Varnam,Axel Visel,Axel Visel,Ray M. Whitlock,Paul Wohnoutka,Crissa K. Wolkey,Victoria Y. Wong,Matthew J.A. Wood,Murat B. Yaylaoglu,Rob Young,Brian L. Youngstrom,Xu Feng Yuan,Bin Zhang,Theresa A. Zwingman,Allan R. Jones +109 more
TL;DR: An anatomically comprehensive digital atlas containing the expression patterns of ∼20,000 genes in the adult mouse brain is described, providing an open, primary data resource for a wide variety of further studies concerning brain organization and function.
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