Journal: Nature Reviews. Genetics

Article Title: Methods and applications for single-cell and spatial multi-omics

doi: 10.1038/s41576-023-00580-2

Figure Lengend Snippet: Spatial multi-ome profiling of tissue samples can be achieved by applying spatial mono-omics assays separately on adjacent or serial tissue sections (part a ) or in a combined way on the same tissue section (parts b – e ). a , Serial fresh-frozen or formalin-fixed paraffin-embedded (FFPE) tissue sections can be analysed using different spatial mono-omic assays, potentially also combining with morphological stainings and annotations on the same or adjacent sections, followed by computational data integration. b , Microfluidic deterministic barcoding strategies in tissue allow next-generation sequencing (NGS)-based spatial multi-omics profiling of transcriptome-plus-proteins, as in DBiT-seq and Spatial-CITE-seq , and epigenome-plus-transcriptome, as in ATAC&RNA-seq and CUT&Tag-RNAseq . Using dual microfluidic chip-based spatial barcoding of poly(A) RNAs together with proteins or epigenome information at the crossroads of chip channels, a spatially barcoded 2D pixel map of the tissue is created. c , Advanced fluorescence in situ hybridization (FISH)-based methods, including MERFISH , , and seqFISH+ , , , allow microscopy-based identification of thousands of transcripts together with genomic loci in single cells, in addition to being compatible with limited protein readouts using fluorescent or DNA-conjugated antibody readout strategies. These high-resolution imaging methods leverage predefined optical barcoding schemes and complex encoding and readout probe designs. d , Array-based assays, including Spatial Transcriptomics (ST) and 10x Genomics Visium , make use of slides with arrayed oligo-dT spots for capturing and spatial barcoding of poly(A) RNAs followed by NGS profiling. This can be combined with upfront haematoxylin and eosin (H&E) staining or limited protein antibody staining and tissue imaging for spatial mapping. In SM-Omics and SPOTS , these technologies have also been shown to be compatible with antibody-derived tag (ADT)-conjugated antibody-based co-profiling of a larger number of proteins. e , NanoString GeoMx digital spatial profiling (DSP) , , allows quantification of RNAs and proteins in specific regions of interest (ROIs) by counting uniquely barcoded oligonucleotides that are covalently linked through a UV-photocleavable linker with probes or antibodies. Tissue marker staining, imaging, ROI selection and illumination by directed UV light causes disintegration of the photocleavable linkers that are collected and profiled by NGS, followed by spatial mapping to the ROIs. cDNA, complementary DNA; gDNA, genomic DNA; OCT, optimal cutting temperature compound; UMI, unique molecular identifier.

Article Snippet: These high-resolution imaging methods leverage predefined optical barcoding schemes and complex encoding and readout probe designs. d , Array-based assays, including Spatial Transcriptomics (ST) and 10x Genomics Visium , make use of slides with arrayed oligo-dT spots for capturing and spatial barcoding of poly(A) RNAs followed by NGS profiling.

Techniques: Formalin-fixed Paraffin-Embedded, Next-Generation Sequencing, Biomarker Discovery, RNA Sequencing, Fluorescence, In Situ Hybridization, Microscopy, Imaging, Staining, Derivative Assay, Marker, Selection

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) Molecular cell type–based neuroanatomy of the goldfish telencephalon. Top: Color scheme shown above for GABAergic and glutamatergic cell types (dendrogram). Center: Eight coronal goldfish sections (goldfish 1), sampled for Visium ST, overlaid with a weighted color map that integrates all goldfish telencephalon cell types. Bottom: Regional parcellation based on color map differences above, each color indicates a different region, and suggested nomenclature annotated by similarity region names according to Northcutt . D , area dorsalis; V , area ventralis; Dc , large-celled subdivision of Dm ; Vsst , ventral Sst; Ppa , nucleus preopticus parvocellularis anterioris; a, anterior; p, posterior; d, dorsal; v, ventral; m, medial; l, lateral. ( B ) Heatmaps of SD (normalized per row) along lateral-medial (left) and dorsal-ventral (right) axes for top axial pattern genes, for goldfish 1 and 2; dots indicate spatial enrichment according to axial color scheme shown above; gray without dot, no enrichment. Right: Summary of axial score per gene (mean of enriched sections). ( C ) Expression of 14 axial-patterned genes across the goldfish telencephalon. Gray, low; red, high.

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Expressing

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) t -SNE visualization of GABAergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type assignment. Right: Expression of three branch-organizing genes. ( B ) All GABA types arranged in dendrogram order (GABA1 to GABA40), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cell type, visualized as pie charts. ( C ) Expression of three branch-organizing genes [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the GABAergic dendrogram for spatial correlation of Visium spots: five scRNA-seq cell types (columns) across eight a.-p. coronal sections (rows).

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Expressing, Marker, Gene Expression

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A ) t -SNE visualization of glutamatergic neurons in the goldfish forebrain. Each dot represents a cell, colored by cell type. ( B ) All glutamatergic types, in dendrogram order (GLUT1 to GLUT48), with top marker gene expression visualized as heatmap (white, high; black, low). Middle: Violin plots, where each dot represents a single cell; maximum expression (UMI) indicated on the right. Bottom: Contribution of four microdissections to each cluster, visualized as pie charts. ( C ) Expression of two branch-organizing genes, NR2F2 and CNR1, visualized on t -SNE [as (A)] and, in ST, eight anterior-posterior telencephalon coronal hemisphere sections. ( D ) Examples across the glutamatergic dendrogram for spatial correlation of Visium spots: four scRNA-seq cell types (columns) across eight anterior-posterior coronal sections (rows).

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Marker, Gene Expression, Expressing

Journal: Science Advances

Article Title: A telencephalon cell type atlas for goldfish reveals diversity in the evolution of spatial structure and cell types

doi: 10.1126/sciadv.adh7693

Figure Lengend Snippet: ( A and B ) t -SNE visualizing comparative species analysis between goldfish and zebrafish telencephalon, with cell types highlighted per species; (A) goldfish and (B) zebrafish. Per cell class, both species’ datasets are integrated (Harmony), followed by DBSCAN clustering. ( C ) Per cell type comparison, scored using KNN classifier. ( D ) Expression of CBLN1, PENK , and SST in the integrated teleostean dataset; dots (cells) colored by species origin. ( E ) Validation of gene expression detected in ST using HCR-FISH. Top row: Corresponding section overviews of genes detected in Visium (left) and HCR (right), where each spot represents a segmented fluorescent cell, colored by normalized expression. Bottom row: Raw fluorescent signal in zoom-ins, as indicated in overview sections.

Article Snippet: ST (Visium, 10x Genomics) is a sequencing-based, transcriptome-wide in situ mRNA detection method; at the loss of cellular resolution, the method retained positional information of mRNA molecules, per 55-μm-diameter capture spots, that are arranged in an array with centers ( X - Y ) 100 μm apart.

Techniques: Comparison, Expressing, Biomarker Discovery, Gene Expression