Companion web sites for published papers and preprints

These papers have companion web sites, usually with a gene browser and data in more convenient formats than what you can get at GEO.

  • Scalable in situ single-cell profiling by electrophoretic capture of mRNA using EEL FISH Lars E. Borm, Alejandro Mossi Albiach, Camiel C. A. Mannens, Jokubas Janusauskas, Ceren Özgün, David Fernández-García, Rebecca Hodge, Francisca Castillo, Charlotte R. H. Hedin, Eduardo J. Villablanca, Per Uhlén, Ed S. Lein, Simone Codeluppi, Sten Linnarsson

    Published in Nature Biotechnology(PDF)

    ★ Supporting data and visualizations.

  • A multimodal cell census and atlas of the mammalian primary motor cortex BRAIN Initiative Cell Census Network (BICCN)

    Published in Nature(PDF)

    ★ Supporting data and visualizations.

  • Comparative cellular analysis of motor cortex in human, marmoset and mouse Trygve E Bakken, Nikolas L Jorstad, Qiwen Hu, Blue B Lake, Wei Tian, Brian E Kalmbach, Megan Crow, Rebecca D Hodge, Fenna M Krienen, Staci A Sorensen, Jeroen Eggermont, Zizhen Yao, Brian D Aevermann, Andrew I Aldridge, Anna Bartlett, Darren Bertagnolli, Tamara Casper, Rosa G Castanon, Kirsten Crichton, Tanya L Daigle, Rachel Dalley, Nick Dee, Nikolai Dembrow, Dinh Diep, Song-Lin Ding, Weixiu Dong, Rongxin Fang, Stephan Fischer, Melissa Goldman, Jeff Goldy, Lucas T Graybuck, Brian R Herb, Xiaomeng Hou, Jayaram Kancherla, Matthew Kroll, Kanan Lathia, Baldur van Lew, Yang Eric Li, Christine S Liu, Hanqing Liu, Jacinta D Lucero, Anup Mahurkar, Delissa McMillen, Jeremy A Miller, Marmar Moussa, Joseph R Nery, Philip R Nicovich, Sheng-Yong Niu, Joshua Orvis, Julia K Osteen, Scott Owen, Carter R Palmer, Thanh Pham, Nongluk Plongthongkum, Olivier Poirion, Nora M Reed, Christine Rimorin, Angeline Rivkin, William J Romanow, Adriana E Sedeño-Cortés, Kimberly Siletti, Saroja Somasundaram, Josef Sulc, Michael Tieu, Amy Torkelson, Herman Tung, Xinxin Wang, Fangming Xie, Anna Marie Yanny, Renee Zhang, Seth A Ament, M Margarita Behrens, Hector Corrada Bravo, Jerold Chun, Alexander Dobin, Jesse Gillis, Ronna Hertzano, Patrick R Hof, Thomas Höllt, Gregory D Horwitz, C Dirk Keene, Peter V Kharchenko, Andrew L Ko, Boudewijn P Lelieveldt, Chongyuan Luo, Eran A Mukamel, António Pinto-Duarte, Sebastian Preissl, Aviv Regev, Bing Ren, Richard H Scheuermann, Kimberly Smith, William J Spain, Owen R White, Christof Koch, Michael Hawrylycz, Bosiljka Tasic, Evan Z Macosko, Steven A McCarroll, Jonathan T Ting, Hongkui Zeng, Kun Zhang, Guoping Feng, Joseph R Ecker, Sten Linnarsson, Ed S Lein

    Published in Nature(PDF)

    ★ Supporting data and visualizations.

  • Molecular architecture of the developing mouse brain Gioele La Manno, Kimberly Siletti, Alessandro Furlan, Daniel Gyllborg, Elin Vinsland, Alejandro Mossi Albiach, Christoffer Mattsson Langseth, Irina Khven, Alex R Lederer, Lisa M Dratva, Anna Johnsson, Mats Nilsson, Peter Lönnerberg, Sten Linnarsson

    Published in Nature(PDF)

    ★ Supporting data and visualizations.

  • Spatial organization of the somatosensory cortex revealed by osmFISH. Codeluppi S, Borm LE, Zeisel A, La Manno G, van Lunteren JA, Svensson CI, Linnarsson S.

    Published in Nature Methods(PDF)

    ★ Supporting data and visualizations.

  • RNA velocity of single cells La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, Lidschreiber K, Kastriti ME, Lönnerberg P, Furlan A, Fan J, Borm LE, Liu Z, van Bruggen D, Guo J, He X, Barker R, Sundström E, Castelo-Branco G, Cramer P, Adameyko I, Linnarsson S, Kharchenko PV.

    Published in Nature(PDF)

    ★ Supporting data and visualizations.

  • Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types. Häring M, Zeisel A, Hochgerner H, Rinwa P, Jakobsson JET, Lönnerberg P, La Manno G, Sharma N, Borgius L, Kiehn O, Lagerström MC, Linnarsson S, Ernfors P.

    Published in Nature Neuroscience(PDF)

    ★ Supporting data and visualizations.

  • Molecular architecture of the mouse nervous system Zeisel A, Hochgerner H, Lönnerberg P, Johnsson A, Memic F, van der Zwan J, Häring M, Braun E, Borm LE, La Manno G, Codeluppi S, Furlan A, Lee K, Skene N, Harris KD, Hjerling-Leffler J, Arenas E, Ernfors P, Marklund U, Linnarsson S.

    Published in Cell(PDF)

    ★ Supporting data and visualizations.

  • Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing. Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S.

    Published in Nature Neuroscience(PDF)

    ★ Supporting data and visualizations.

  • Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells Gioele La Manno, Daniel Gyllborg, Simone Codeluppi, Kaneyasu Nishimura, Carmen Salto, Amit Zeisel, Lars E. Borm, Simon R.W. Stott, Enrique M. Toledo, J. Carlos Villaescusa, Peter Lönnerberg, Jesper Ryge, Roger A. Barker, Ernest Arenas, and Sten Linnarsson

    Published in Cell(PDF)

    ★ Supporting data and visualizations.

  • Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity Simon Joost, Amit Zeisel, Tina Jacob, Xiaoyan Sun, Gioele La Manno, Peter Lönnerberg, Sten Linnarsson*, Maria Kasper*

    Published in Cell Systems(PDF)

    ★ Supporting data and visualizations.

  • Visceral motor neuron diversity delineates a cellular basis for nipple- and pilo-erection muscle control Alessandro Furlan, Gioele La Manno, Moritz Lübke, Martin Häring, Hind Abdo, Hannah Hochgerner, Jussi Kupari, Dmitry Usoskin, Matti S Airaksinen, Guillermo Oliver, Sten Linnarsson* and Patrik Ernfors*

    Published in Nature Neuroscience(PDF)

    ★ Supporting data and visualizations.

  • Origin, fate and dynamics of macrophages at central nervous system interfaces. Goldmann T, Wieghofer P, Jordão MJ, Prutek F, Hagemeyer N, Frenzel K, Amann L, Staszewski O, Kierdorf K, Krueger M, Locatelli G, Hochgerner H, Zeiser R, Epelman S, Geissmann F, Priller J, Rossi FM, Bechmann I, Kerschensteiner M, Linnarsson S, Jung S, Prinz M.

    Published in Nature Immunology(PDF)

    ★ Supporting data and visualizations.

  • Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Marques S, Zeisel A, Codeluppi S, van Bruggen D, Mendanha Falcão A, Xiao L, Li H, Häring M, Hochgerner H, Romanov RA, Gyllborg D, Muñoz-Manchado AB, La Manno G, Lönnerberg P, Floriddia EM, Rezayee F, Ernfors P, Arenas E, Hjerling-Leffler J, Harkany T, Richardson WD, Linnarsson S*, Castelo-Branco G*.

    Published in Science(PDF)

    ★ Supporting data and visualizations.

  • Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Zeisel A, Muñoz-Manchado AB, Codeluppi S, Lönnerberg P, La Manno G, Juréus A, Marques S, Munguba H, He L, Betsholtz C, Rolny C, Castelo-Branco G, Hjerling-Leffler J, Linnarsson S.

    Published in Science(PDF)

    ★ Supporting data and visualizations.

  • Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Usoskin D, Furlan A, Islam S, Abdo H, Lönnerberg P, Lou D, Hjerling-Leffler J, Haeggström J, Kharchenko O, Kharchenko PV, Linnarsson S*, Ernfors P.*

    Published in Nature Neuroscience(PDF)

    ★ Supporting data and visualizations.

Raw sequence data

All raw data for our published work is available at GEO.