Transcriptomics articles within Nature

Featured

  • 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

  • Article |

    Single-nucleus RNA-sequencing analyses of brain from humans, macaques, marmosets, mice and ferrets reveal diverse ways that interneuron populations have changed during evolution.

    • Fenna M. Krienen
    • , Melissa Goldman
    •  & Steven A. McCarroll

  • Article |

    Single-cell RNA-sequencing analysis of embryogenesis and X chromosome inactivation in the opossum (Monodelphis domestica) resolves the developmental trajectory of a marsupial, and sheds light on the evolution of embryogenesis in mammals.

    • Shantha K. Mahadevaiah
    • , Mahesh N. Sangrithi
    •  & James M. A. Turner

  • News & Views |

    The third phase of the Encyclopedia of DNA Elements (ENCODE) project has generated the most comprehensive catalogue yet of the functional elements that regulate our genes.

    • Chung-Chau Hon
    •  & Piero Carninci

  • Perspective |

    The authors summarize the history of the ENCODE Project, the achievements of ENCODE 1 and ENCODE 2, and how the new data generated and analysed in ENCODE 3 complement the previous phases.

    • Federico Abascal
    • , Reyes Acosta
    •  & Richard M. Myers

  • Article
    | Open Access

    ChIP–seq and CETCh–seq data are used to analyse binding maps for 208 transcription factors and other chromatin-associated proteins in a single human cell type, providing a comprehensive catalogue of the transcription factor landscape and gene regulatory networks in these cells.

    • E. Christopher Partridge
    • , Surya B. Chhetri
    •  & Eric M. Mendenhall

  • Article |

    Bulk RNA sequencing of organs and plasma proteomics at different ages across the mouse lifespan is integrated with data from the Tabula Muris Senis, a transcriptomic atlas of ageing mouse tissues, to describe organ-specific changes in gene expression during ageing.

    • Nicholas Schaum
    • , Benoit Lehallier
    •  & Tony Wyss-Coray

  • Article
    | Open Access

    Single-cell RNA sequencing identifies the pattern of gene expression during lineage progression in endosymbiotic cells of the fast-growing soft coral Xenia, revealing principles that underlie uptake and maintenance of endosymbionts by this coral.

    • Minjie Hu
    • , Xiaobin Zheng
    •  & Yixian Zheng

  • Article
    | Open Access

    A novel variant annotation metric that quantifies the level of expression of genetic variants across tissues is validated in the Genome Aggregation Database (gnomAD) and is shown to improve rare variant interpretation.

    • Beryl B. Cummings
    • , Konrad J. Karczewski
    •  & Daniel G. MacArthur

  • Article |

    Single-cell RNA sequencing is used to generate a dataset covering all major human organs in both adult and fetal stages, enabling comparison with similar datasets for mouse tissues.

    • Xiaoping Han
    • , Ziming Zhou
    •  & Guoji Guo

  • News & Views |

    Whether cell types in the brain have been conserved during evolution is not clear. A comparison of the molecular recipes that define brain cell types in humans and mice reveals similarities and differences between species.

    • Matthew G. Keefe
    •  & Tomasz J. Nowakowski

  • Letter |

    Species of the eukaryotic phylum Rhodelphidia are non-photosynthetic, flagellate predators with gene-rich genomes, in contrast to their closely related sister lineage—the red algae—which are immotile, typically photoautotrophic and have relatively small intron-poor genomes and reduced metabolism.

    • Ryan M. R. Gawryluk
    • , Denis V. Tikhonenkov
    •  & Patrick J. Keeling

  • News & Views |

    An analysis of gene expression in sea-squirt embryos at different stages of development deepens our understanding of how the body plans of vertebrates might have evolved from those of less complex animals.

    • Noriyuki Satoh

  • Article |

    Comprehensive single-cell transcriptomes in the proto-vertebrate Ciona intestinalis identified provisional gene networks for 41 different neural subtypes, providing insights into the swimming circuit of tadpoles and the evolution of the vertebrate telencephalon.

    • Chen Cao
    • , Laurence A. Lemaire
    •  & Kai Chen

  • News & Views |

    A method for detecting mutations and measuring gene-expression levels in the same cell has enabled an investigation into the effects of mutations in a specific gene on the emergence of a form of blood cancer.

    • Siddharth Raju
    •  & Chun Jimmie Ye

  • Article |

    A transcriptome dataset from seven organs and seven mammalian species throughout development is used to analyse the expression of long noncoding RNAs in tissues within and between species, and at different stages of organ development.

    • Ioannis Sarropoulos
    • , Ray Marin
    •  & Henrik Kaessmann

  • News & Views |

    Knowing the gene-expression pattern of individual cells can unlock their identity. A refined method for generating cellular RNA profiles offers a way to obtain such data at a high level of spatial resolution in intact tissues.

    • Samantha A. Morris

  • Article |

    Data from single-cell combinatorial-indexing RNA-sequencing analysis of 2 million cells from mouse embryos between embryonic days 9.5 and 13.5 are compiled in a cell atlas of mouse organogenesis, which provides a global view of developmental processes occurring during this critical period.

    • Junyue Cao
    • , Malte Spielmann
    •  & Jay Shendure

  • Article |

    A set of 34 excised introns in Saccharomyces cerevisiae, characterized by having a short distance between the lariat branch point and the 3′ splice site, have a biological function within the TOR growth-signalling network.

    • Jeffrey T. Morgan
    • , Gerald R. Fink
    •  & David P. Bartel

  • Letter |

    Allele-specific single-cell RNA sequencing provides insights into transcription kinetics, with data indicating that core promoter sequences affect burst size, whereas enhancers mainly affect burst frequency.

    • Anton J. M. Larsson
    • , Per Johnsson
    •  & Rickard Sandberg

  • Letter |

    Ikzf2, which encodes the transcription factor Helios, is identified as a crucial regulator of gene expression in maturing cochlear outer hair cells, and overexpression of Ikzf2 in inner hair cells induces prestin expression and electromotility.

    • Lauren Chessum
    • , Maggie S. Matern
    •  & Ronna Hertzano

  • News & Views |

    RNA sequencing of thousands of single cells located at the interface between mother and fetus in early pregnancy reveals remarkable complexity in the cell types and regulatory networks that support reproduction.

    • Sumati Rajagopalan
    •  & Eric O. Long

  • News & Views |

    A single-cell sequencing study reveals how different types of neuron are distributed in the brain. An analysis then demonstrates how these data can improve our understanding of neuronal functions.

    • Aparna Bhaduri
    •  & Tomasz J. Nowakowski

  • Article |

    Single-cell transcriptomics of more than 20,000 cells from two functionally distinct areas of the mouse neocortex identifies 133 transcriptomic types, and provides a foundation for understanding the diversity of cortical cell types.

    • Bosiljka Tasic
    • , Zizhen Yao
    •  & Hongkui Zeng

  • News & Views |

    RNA sequencing of single cells in the mammalian trachea reveals a previously unknown airway cell that expresses genes involved in fluid and solute balance, and that might play a part in cystic fibrosis.

    • Kyle J. Travaglini
    •  & Mark A. Krasnow

  • News & Views |

    The mouse pancreas adopts a pre-inflammatory state in response to a chemical injury or the loss of one copy of the gene Nr5a2. This state might predispose mice, and possibly humans, to pancreatitis and pancreatic cancer.

    • L. Charles Murtaugh
    •  & Raymond J. MacDonald

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