Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

By C. Eng, M. Lawson, Qian Zhu, Ruben Dries, N. Koulena, Yodai Takei, Jina Yun, Christopher J. Cronin, Christoph Karp, Guocheng Yuan and 1 more. Nature, 2019

1,655 citations recorded by the source corpus.

Imaging the transcriptome in situ with high accuracy has been a major challenge in single-cell biology, which is particularly hindered by the limits of optical resolution and the density of transcripts in single cells1–5. Here we demonstrate an evolution of sequential fluorescence in situ hybridization (seqFISH+). We show that seqFISH+ can image mRNAs for 10,000 genes in single cells—with high accuracy and sub-diffraction-limit resolution—in the cortex, subventricular zone and olfactory bulb of mouse brain, using a standard confocal microscope. The transcriptome-level profiling of seqFISH+ allows unbiased identification of cell classes and their spatial organization in tissues. In addition, seqFISH+ reveals subcellular mRNA localization patterns in cells and ligand–receptor pairs across neighbouring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery-driven studies of biological processes in situ. seqFISH+, an evolution of sequential fluorescence in situ hybridization with super-resolution imaging capabilities, is used to image mRNAs of 10,000 genes in cultured cells and mouse brain slices, demonstrating the ability to generate spatial atlases and to perform discovery-driven studies in situ.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/159f42b03579769c40ede738831c7ad5e98369e1

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Citations in the corpus

• High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue (2020, neutral): “Early attempts towards spatial transcriptomics were based on multiplexed fluorescent in situ hybridization (Chen et al., 2015; Eng et al., 2019; Lubeck et al., 2014; Perkel, 2019).”
• Screening cell–cell communication in spatial transcriptomics via collective optimal transport (2023, methodology): “To demonstrate downstream analyses of CCC, we first studied seqFISH+ (sequential fluorescence in situ hybridization) data of mouse secondary somatosensory cortex with 10,000 genes measured in 523 individual cells 18 (Fig.”
• Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression (2019, methodology): “used 3 independent sets of 80-bit, Hamming weight 4, error-correcting codes [a kind that can also be considered as a 4-unit base-20 code (7)] to detect ∼10,000 genes with 3-color imaging and 80 rounds of hybridization.”
• Spatial components of molecular tissue biology (2022, neutral): “We distinguish two main influences on cell states in the spatial context (‘dependency classes’): direct cell–cell communication and tissue context (Fig.”
• Spatially informed clustering, integration, and deconvolution of spatial transcriptomics with GraphST (2023, neutral): “Meanwhile, fl uorescent in situ hybridization (FISH)-based methods are capable of achieving subcellular resolution but lack genome-scale gene coverage, with the latest seqFish having a 10,000 gene limit 25 .”