Read this week's free-access protocol

Complex-centric proteome profiling

Browse Articles

  • Protocol |

    GOTI (genome-wide off-target analysis by two-cell embryo injection) detects off-target mutations of CRISPR–Cas9-based genome editing and base editing. One blastomere of a two-cell mouse embryo is edited so that edited and unedited cells from the same genetic background can be compared.

    • Erwei Zuo
    • , Yidi Sun
    • , Wu Wei
    • , Tanglong Yuan
    • , Wenqin Ying
    • , Hao Sun
    • , Liyun Yuan
    • , Lars M. Steinmetz
    • , Yixue Li
    •  & Hui Yang
  • Protocol |

    This protocol describes a microfluidic platform for dynamic high-throughput analysis of the phenotypes of single cells. Cell-surface markers and secreted proteins are quantified and characterized by fluorescence detection using tailored immunoassays.

    • Yacine Bounab
    • , Klaus Eyer
    • , Sophie Dixneuf
    • , Magda Rybczynska
    • , Cécile Chauvel
    • , Maxime Mistretta
    • , Trang Tran
    • , Nathan Aymerich
    • , Guilhem Chenon
    • , Jean-François Llitjos
    • , Fabienne Venet
    • , Guillaume Monneret
    • , Iain A. Gillespie
    • , Pierre Cortez
    • , Virginie Moucadel
    • , Alexandre Pachot
    • , Alain Troesch
    • , Philippe Leissner
    • , Julien Textoris
    • , Jérôme Bibette
    • , Cyril Guyard
    • , Jean Baudry
    • , Andrew D. Griffiths
    •  & Christophe Védrine
  • Protocol |

    This protocol describes the MAC-tag approach, which combines affinity purification and biotinylation identification proximity labeling in a single tag. Binding proteins are identified by liquid chromatography–mass spectrometry, followed by visualization of protein localization using an online platform.

    • Xiaonan Liu
    • , Kari Salokas
    • , Rigbe G. Weldatsadik
    • , Lisa Gawriyski
    •  & Markku Varjosalo
  • Protocol |

    Embryonic stem cells undergo CRISPR–Cas9-mediated editing and are then used to reconstitute forebrain regions in mouse chimeras via neural blastocyst complementation.

    • Hai-Qiang Dai
    • , Zhuoyi Liang
    • , Amelia N. Chang
    • , Aimee M. Chapdelaine-Williams
    • , Beatriz Alvarado
    • , Alex A. Pollen
    • , Frederick W. Alt
    •  & Bjoern Schwer
  • Protocol Extension |

    Flow cytometry is used to track dynamics in microbial communities and link these changes with ecological parameters. This protocol describes how to prepare a fixed microbial cytometric mock community to standardize results over large-scale studies.

    • Nicolas Cichocki
    • , Thomas Hübschmann
    • , Florian Schattenberg
    • , Frederiek-Maarten Kerckhof
    • , Jörg Overmann
    •  & Susann Müller
  • Protocol |

    Formalin fixation and paraffin embedding (FFPE) of human tissue is a central strategy for preserving pathological specimens. This protocol describes how to process these specimens for spatially resolved LC-MS by laser-capture microdissection.

    • Katarzyna Buczak
    • , Joanna M. Kirkpatrick
    • , Felicia Truckenmueller
    • , Deolinda Santinha
    • , Lino Ferreira
    • , Stephanie Roessler
    • , Stephan Singer
    • , Martin Beck
    •  & Alessandro Ori
  • Protocol |

    This protocol provides standardized laboratory manufacturing practices to select, cultivate and purify bacteriophages for human clinical applications. The procedure covers all stages from phage isolation and characterization to quality control.

    • Tiffany Luong
    • , Ann-Charlott Salabarria
    • , Robert A. Edwards
    •  & Dwayne R. Roach

Collection

The 3D genome

V. Summersby

The 3D genome

This collection includes recent articles from across the Nature group of journals and showcases both the latest advances in the methodologies used to study genome organization, and our recent understanding of how genome organization and nuclear architecture regulate gene expression, cell fate and cell function in physiology and disease.

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