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

Abstract

Imaging the transcriptome in situ with high accuracy has been a major challenge in single cell biology, particularly hindered by the limits of optical resolution and the density of transcripts in single cells [1][2][3][4][5] . Here, we demonstrate seqFISH+, that can image the mRNAs for 10,000 genes in single cells with high accuracy and sub-diffraction-limit resolution, in the mouse brain cortex, subventricular zone, and the olfactory bulb, 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 neighboring cells. This technology demonstrates the ability to generate spatial cell atlases and to perform discovery-driven studies of biological processes in situ. Spatial genomics, the analysis of the transcriptome and other genomic information directly in the native context of tissues, is crucial to many fields in biology, including neuroscience and developmental biology. Pioneering work in single molecule Fluorescence in situ Reprints and permissions information is available at www.nature.com/reprintsUsers may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://

A Single‐Cell Perspective of the Mammalian Liver in Health and Disease

“…Single‐cell genomics offer powerful tools for unraveling cell heterogeneity in complex organs, the nature of intercellular crosstalk, and disease‐associated cellular reprogramming with unprecedented resolution. New technologies are being developed to further expand single‐cell analysis to include spatial information of cells in their native tissue context, such as sequential FISH and spatially barcoded transcriptomic analysis . In addition, multimodal and integrated methods are available for high‐resolution mapping of chromatin state (DNA methylation, chromatin accessibility, histone modifications), genome sequence, and cell‐surface protein expression in combination with single‐cell transcriptomic analysis, as discussed in a recent review .…”

“…New technologies are being developed to further expand single-cell analysis to include spatial information of cells in their native tissue context, such as sequential FISH and spatially barcoded transcriptomic analysis. (29,30) In addition, multimodal and integrated methods are available for high-resolution mapping of chromatin state (DNA methylation, chromatin accessibility, histone modifications), genome sequence, and cell-surface protein expression in combination with single-cell transcriptomic analysis, as discussed in a recent review. (31) These emerging tools are expected to reveal multidimensional details of the liver microenvironment in physiological and disease states.…”

A method for transcriptome‐wide gene expression quantification in intact tissues

“…To screen which regulatory pathways are affected by cell–cell interactions has been very challenging, a new technology published in the March issue of Nature by Eng et al . points toward a scalable solution . The Improved sequential fluorescence in situ hybridization (SeqFISH+) method allows quantitative gene expression measurements of 10 000 genes in situ within intact tissue samples at single‐cell resolution, within thousands of single cells.…”

“…This experimental pipeline will, however, not be able to identify which pathways are modulated by local tissue neighborhood. Using their transcriptome‐wide multiplexed single‐molecule fluorescent in situ hybridization method, SeqFISH+, the authors identified without bias a large number of cell types in the mouse cortex and olfactory bulb . From these inferred cell identities, they were able to quantify the degree of colocalization of cell types (e.g.…”

“…Using their transcriptome-wide multiplexed single-molecule fluorescent in situ hybridization method, SeqFISH+, the authors identified without bias a large number of cell types in the mouse cortex and olfactory bulb. 1 From these inferred cell identities, they were able to quantify the degree of colocalization of cell types (e.g. identifying two types of neuroblasts which are preferentially in contact).…”