Transcriptomics articles within Nature

Featured

  • Article
    | Open Access

    Combining single-cell RNA-sequencing with high-resolution multiplexed error-robust fluorescence in situ hybridization reveals in detail the cellular interactions and specialization of cardiac cell types that form and remodel the human heart.

    • Elie N. Farah
    • , Robert K. Hu
    •  & Neil C. Chi
  • Article
    | Open Access

    Spatial and single-cell transcriptomic analyses of the mouse basolateral amygdala reveal transcriptomic signatures, spatial resolution and interactions of cells that constitute the memory engram, including crucial neuron–astrocyte interactions.

    • Wenfei Sun
    • , Zhihui Liu
    •  & Stephen R. Quake
  • News & Views |

    A tool that tags individual cells in a tissue with a unique barcode means that the gene-expression profile of each cell can be plotted in its original location. This allows spatial information to be captured at single-cell resolution.

    • Patrik L. Ståhl
  • News & Views Forum |

    In a huge collaborative effort, millions of cells in the mouse brain have been mapped in detail. Two scientists examine the resulting wealth of insights into gene regulation in brain cells, neuronal connections and how our own brains evolved.

    • Maria Antonietta Tosches
    •  & Heather J. Lee
  • Article
    | Open Access

    To construct a comprehensive atlas of cell types in each brain structure, we paired high-throughput single-nucleus RNA sequencing with Slide-seq, a recently developed spatial transcriptomics method with near-cellular resolution, across the entire mouse brain.

    • Jonah Langlieb
    • , Nina S. Sachdev
    •  & Evan Z. Macosko
  • Article
    | Open Access

    Using single-cell and spatial transcriptomics, human embryonic limb development across space and time and the diversification and cross-species conservation of cells are demonstrated.

    • Bao Zhang
    • , Peng He
    •  & Sarah A. Teichmann
  • Article
    | Open Access

    We present the ‘zebrafish single-cell atlas of perturbed embryos’, single-cell trancriptomic data of developing zebrafish embryos across various timepoints and with genetic perturbations.

    • Lauren M. Saunders
    • , Sanjay R. Srivatsan
    •  & Cole Trapnell
  • Article
    | Open Access

    In situ spatial transcriptomic analysis of more than 1 million cells are used to create a 200-nm-resolution spatial molecular atlas of the adult mouse central nervous system and identify previously unknown tissue architectures.

    • Hailing Shi
    • , Yichun He
    •  & Xiao Wang
  • Article
    | Open Access

    An in vivo single-cell CRISPR screening method identifies transcriptional phenotypes of 22q11.2 deletion syndrome associated with a broad dysregulation of a class of disease susceptibility genes that are important for RNA processing and synaptic function.

    • Antonio J. Santinha
    • , Esther Klingler
    •  & Randall J. Platt
  • Technology Feature |

    By combining single-cell sequencing with methods to map the spatial location of gene expression, scientists are unravelling the extraordinary cellular diversity of the brain.

    • Diana Kwon
  • Article
    | Open Access

    Single-cell transcriptomics and in vivo challenge models establish a key role for the aryl hydrocarbon receptor in regulating the function of enteric endothelial cells in response to environmental cues.

    • Benjamin G. Wiggins
    • , Yi-Fang Wang
    •  & Chris Schiering
  • News & Views |

    The HuBMAP consortium has generated spatially resolved cell atlases for the human intestine, kidney and placenta, which enable analysis of tissue organization in unprecedented detail.

    • Roser Vento-Tormo
    •  & Roser Vilarrasa-Blasi
  • Article
    | Open Access

    Single-cell and spatial transcriptomic analysis of eight human heart tissues reveals the cellular profiles and tissue architecture of niches including the cardiac conduction system, and a new tool, drug2cell, identifies drug target expression.

    • Kazumasa Kanemaru
    • , James Cranley
    •  & Sarah A. Teichmann
  • News & Views |

    The compilation and analysis of a compendium of single-cell RNA-sequencing studies across various cancers reveals recurring gene-expression programs that underpin tumour heterogeneity.

    • Raymond W. S. Ng
    •  & Sydney M. Shaffer
  • Article
    | Open Access

    Computational and machine-learning approaches that integrate genomic and transcriptomic variation from paired primary and metastatic non-small cell lung cancer samples from the TRACERx cohort reveal the role of transcriptional events in tumour evolution.

    • Carlos Martínez-Ruiz
    • , James R. M. Black
    •  & Nicholas McGranahan
  • Article |

    Provora is an ancient supergroup of microbial predators that are genetically, morphologically and behaviourally distinct from other eukaryotes, and comprise two divergent clades of predators—Nebulidia and Nibbleridia—that differ fundamentally in ultrastructure, behaviour and gene content.

    • Denis V. Tikhonenkov
    • , Kirill V. Mikhailov
    •  & Patrick J. Keeling
  • Article
    | Open Access

    RNA sequencing reveals widespread transcriptomic changes across the cerebral cortex in autism spectrum disorder, including primary sensory regions, in addition to association regions, as well as an attenuation of regional identity.

    • Michael J. Gandal
    • , Jillian R. Haney
    •  & Daniel H. Geschwind
  • Article
    | Open Access

    Live-seq, a single-cell transcriptome profiling approach that preserves cell viability during RNA extraction using fluidic force microscopy, can address a range of biological questions by transforming scRNA-seq from an end-point to a temporal analysis approach.

    • Wanze Chen
    • , Orane Guillaume-Gentil
    •  & Bart Deplancke
  • Article |

    A time-resolved high-resolution map of human cardiac remodelling after myocardial infarction, integrating single-cell transcriptomic, chromatin accessibility and spatial transcriptomic data, provides a valuable resource for the field.

    • Christoph Kuppe
    • , Ricardo O. Ramirez Flores
    •  & Rafael Kramann
  • Article |

    cis-RNA editing quantitative trait loci, which are associated with immunogenic double-stranded RNAs, underlie genome-wide association study variants in common autoimmune and inflammatory diseases.

    • Qin Li
    • , Michael J. Gloudemans
    •  & Jin Billy Li
  • News & Views |

    A combination of functional imaging and gene-expression profiling in brain tissue has been used to unravel the properties of 35 subtypes of neuron in mice, revealing a gene-expression axis that governs each subtype’s activity.

    • Hongkui Zeng
    •  & Saskia E. J. de Vries
  • Article |

    The systematic categorization of human enhancers by their cofactor dependencies provides a conceptual framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes.

    • Christoph Neumayr
    • , Vanja Haberle
    •  & Alexander Stark
  • News & Views |

    The trigeminal nerve has a key role in migraine. An atlas of cell types and gene-expression profiles for cells in this nerve in mice and humans promises to improve our understanding of head pain.

    • Philip R. Holland
    •  & Peter J. Goadsby
  • Article
    | Open Access

    Experiments in yeast show that introns have a role in inducing phenotypic heterogeneity and that intron-mediated regulation of ribosomal proteins confers a fitness advantage by enabling yeast populations to diversify under nutrient-scarce conditions.

    • Martin Lukačišin
    • , Adriana Espinosa-Cantú
    •  & Tobias Bollenbach
  • Article |

    A transcriptomics study demonstrates cell-type-specific responses to differentially aged blood and shows young blood to have restorative and rejuvenating effects that may be invoked through enhanced mitochondrial function.

    • Róbert Pálovics
    • , Andreas Keller
    •  & Tony Wyss-Coray
  • Article |

    A study describes single-cell characterization of the human cerebrovasculature, revealing human-specific transcriptomic signatures and providing insights into transcriptional changes associated with Huntington’s disease.

    • Francisco J. Garcia
    • , Na Sun
    •  & Myriam Heiman
  • News & Views |

    Cell-free RNA transcripts in maternal blood can be analysed to monitor the progression of pregnancy and to predict a potentially harmful pregnancy-specific condition called pre‑eclampsia.

    • Lydia L. Shook
    •  & Andrea G. Edlow
  • News & Views Forum |

    An atlas of the cell types found in the motor cortex of the brain has been built using various types of data. Two neuroscientists explain the technological feats involved in the project, as well as the utility of the resource for future research.

    • Johan Winnubst
    •  & Silvia Arber
  • Review Article |

    This review describes the state of spatial transcriptomics technologies and analysis tools that are being used to generate biological insights in diverse areas of biology.

    • Anjali Rao
    • , Dalia Barkley
    •  & Itai Yanai
  • Article |

    A comprehensive single-cell transcriptomic atlas of the mouse brain between gastrulation and birth identifies hundreds of cellular states and reveals the spatiotemporal organization of brain development.

    • Gioele La Manno
    • , Kimberly Siletti
    •  & Sten Linnarsson
  • Article |

    Single-nucleus transcriptomes of frontal cortex and choroid plexus samples from patients with COVID-19 reveal pathological cell states that are similar to those associated with human neurodegenerative diseases and chronic brain disorders.

    • Andrew C. Yang
    • , Fabian Kern
    •  & Tony Wyss-Coray
  • Research Summary |

    Use of chromatin immunoprecipitation with exonuclease treatment (ChIP–exo) determines the positional organization of hundreds of chromosomal proteins throughout the Saccharomyces cerevisiae genome. The resulting ultra-high-resolution map provides insight into the regulation of genes, enhancers, replication origins, centromeres, subtelomeres and transposons.

    • B. Franklin Pugh