Fluorescence in situ hybridization articles within Nature Communications

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  • Article
    | Open Access

    Application of multiplexed RNA in situ mapping techniques to human tissues remains challenging. Here, the authors report DART-FISH, a padlock probe-based technology capable of profiling large numbers of genes in centimetre-sized human tissue sections.

    • Kian Kalhor
    • , Chien-Ju Chen
    •  & Kun Zhang

  • Article
    | Open Access

    Gene selection for spatial transcriptomics is currently not optimal. Here the authors report PERSIST, a flexible deep learning framework that uses existing scRNA-seq data to identify gene targets for spatial transcriptomics; they show this allows you to capture more information with fewer genes.

    • Ian Covert
    • , Rohan Gala
    •  & Su-In Lee

  • Article
    | Open Access

    Spatial analysis of microbiomes at single cell resolution is challenging. Here the authors report a highly multiplexed method for spatial profiling, sequential error-robust fluorescence in situ hybridisation (SEER-FISH), and show that this allows mapping of microbial communities at micron-scale.

    • Zhaohui Cao
    • , Wenlong Zuo
    •  & Lei Dai

  • Article
    | Open Access

    Methods for jointly analysing the different spatial data modalities in 3D are lacking. Here the authors report the computational framework STACI (Spatial Transcriptomic data using over-parameterized graph-based Autoencoders with Chromatin Imaging data) which they apply to an Alzheimer’s disease mouse model.

    • Xinyi Zhang
    • , Xiao Wang
    •  & Caroline Uhler

  • Article
    | Open Access

    Single-cell RNA-seq reveals the cellular heterogeneity in development and disease. Here the authors present a single-nucleus RNA-seq2 that allows deep characterization of nuclei isolated from frozen archived tissues, apply it for transcriptional profiling of individual hepatocytes, and determine a functional crosstalk between liver zonation and ploidy.

    • M. L. Richter
    • , I. K. Deligiannis
    •  & C. P. Martinez-Jimenez

  • Article
    | Open Access

    Inaccurate cell segmentation has been the major problem for cell-type identification and tissue characterization of the in situ spatially resolved transcriptomics data. Here we show a robust cell segmentation-free computational framework (SSAM), for identifying cell types and tissue domains in 2D and 3D.

    • Jeongbin Park
    • , Wonyl Choi
    •  & Naveed Ishaque

  • Article
    | Open Access

    The liver possesses the ability to regenerate following sudden injury. Here, the authors use single-cell RNA-sequencing and in situ transcriptional analyses to identify a new phase of liver regeneration in mice aimed at maintaining essential functions throughout the regenerative process.

    • Chad M. Walesky
    • , Kellie E. Kolb
    •  & Wolfram Goessling

  • Article
    | Open Access

    The mechanism underlying packaging of the 8 segments of the influenza virus genome into virions is not well understood. Here, the authors use a multiplexed FISH assay to monitor the 8 segments in parallel in infected cells suggesting bundling routes during the packaging process.

    • Ivan Haralampiev
    • , Simon Prisner
    •  & Andreas Herrmann

  • Article
    | Open Access

    Astrocytes are a major cell type in the central nervous system. Using single cell transcriptome sequencing, the authors identify multiple astrocyte subtypes in the adult mouse CNS, which map to distinct spatial locations and show correlations to cell morphology and physiology.

    • Mykhailo Y. Batiuk
    • , Araks Martirosyan
    •  & Matthew G. Holt

  • Article
    | Open Access

    Automated analysis of RNA localisation in smFISH data has been elusive. Here, the authors simulate and use a large dataset of images to design and validate a framework for highly accurate classification of sub-cellular RNA localisation patterns from smFISH experiments.

    • Aubin Samacoits
    • , Racha Chouaib
    •  & Florian Mueller

  • Article
    | Open Access

    FISH-based techniques to image and count mRNA in single cells can be limited by the photophysical properties of organic dyes. Here the authors develop photostable quantum dot FISH probes for multiplexed imaging.

    • Yang Liu
    • , Phuong Le
    •  & Andrew M. Smith

  • Article
    | Open Access

    When perceiving new stimuli, organisms need to distinguish between threats versus harmless stimuli. Here, the authors find a set of cells in the lateral amygdala that is required to discriminate or generalize new auditory stimuli based on similarity to previously fear-associate sounds.

    • Anna Grosso
    • , Giulia Santoni
    •  & Benedetto Sacchetti

  • Article
    | Open Access

    Neural crest cells arise within the central nervous system, then migrate and contribute to a variety of cell types. Here, the authors use multiplex transcript analysis at single cell  resolution to define neural crest and neural subpopulations within the avian neural tube, including a neural crest stem cell niche.

    • Antti Lignell
    • , Laura Kerosuo
    •  & Marianne E. Bronner

  • Article
    | Open Access

    The spatial organization of the genome within the nucleus impacts many processes. Here the authors combine oligo-based DNA FISH with single-molecule super-resolution microscopy to image single-copy genomic regions and, taking advantage of SNPs, distinguish allelic regions of homologous chromosomes.

    • Brian J. Beliveau
    • , Alistair N. Boettiger
    •  & Chao-ting Wu

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