Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) Overall approach for generating iST data. (b) Different amplification approaches for Xenium, MERSCOPE, and CosMx. (c) Overview of the tissue types and numbers of cores used in this study. BlC = bladder cancer, BrC = breast cancer, CRC = colorectal cancer, HNSCC = head and neck squamous cell carcinoma, Mel = Melanoma, NSCLC = non-small cell lung cancer, OvC = ovarian cancer. (d) DAPI images from the Xenium run of each TMA, including tumors (top) and normal tissues (bottom) (e) The number of common target genes in each panel used in this study. (f) Overall timeline of the imaging days for each study. Day = 0 corresponds to the day of slicing. † denotes the MERSCOPE breast and lung panels acquired with a 5 µm imaging thickness, thinner than manufacturer instructions.

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques: Amplification, Imaging

Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) Scatter plots of cumulative gene expression levels (natural log transformed) of shared genes between two panels within each platforms, captured from matched tissue cores. Column 1: Xenium breast vs. Xenium lung; Column 2: Xenium breast vs. Xenium multi-tissue; Column 3: MERSCOPE breast round 1(5 µm) vs. MERSCOPE breast round 2(10 µm). Each data point corresponds to a TMA core. (b) Scatter plots of gene expression levels (natural log transformed) of every shared gene between two cores of the same tissue type from the same patient. In this example, cores are from breast cancer tissue. Each data point corresponds to a gene. (c) Heatmap of correlation coefficient expressed as Pearson’s r values, indicating good core-to-core or sample-to-sample reproducibility. Core pairs are selected from same tissue/tumor type from the same patients.

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques: Gene Expression, Transformation Assay

Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) Scatter plots of summed gene expression levels (natural log transformed) of every shared gene between Xenium (breast/lung) and CosMx (1k) data, captured from matched tumor TMA cores. Each data point corresponds to a gene. (b) Same as (a) but between MERSCOPE (breast/lung) and CosMx(1k). (c) Same as (a) but between Xenium(breast/lung) and MERSCOPE(breast/lung). (d) Same as (a) but between Xenium(multi-tissue) and CosMx(1k). (e) Bar plot of percentage of all transcripts corresponding to genes relative to the total number of calls (including negative control probes and unused barcodes) averaged across cores of the same tissue type. Results are presented by panel including breast, lung, and multi-tissue panels from Xenium; breast and lung panels from MERSCOPE; and multi-tissue 1k panel from CosMx. (f) Bar plot of false discovery rate (FDR) where FDR(%) = (blank barcode calls / total transcript calls) x (Number of panel genes/Number of blank barcode) x 100. FDR values were log 10 transformed to better show the differences between panels. (g) Same as (f) but using negative control probes to replace blank barcodes. MERSCOPE is missing in this bar plot as it does not have negative control probe by design. (h) Bar plot of number of genes detected above noise, estimated as two standard deviations above average of the negative control probes. (i) Same as (h) but normalized to the number of genes in a panel. † denotes the MERSCOPE lung panel acquired with a 5 µm imaging thickness.

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques: Gene Expression, Transformation Assay, Negative Control, Imaging

Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) Scatter plots of summed gene expression levels (natural log transformed) of every shared gene between Xenium (breast/lung) and CosMx (1k) data, captured from matched normal tissue TMA cores. Each data point corresponds to a gene. (b) Same as (a) but between MERSCOPE (breast/lung) and CosMx(1k). (c) Same as (a) but between Xenium(breast/lung) and MERSCOPE(breast/lung). (d) Same as (a) but between Xenium(multi-tissue) and CosMx(1k). † denotes the MERSCOPE lung panel acquired with a 5 µm imaging thickness.

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques: Gene Expression, Transformation Assay, Imaging

Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) Scatter plots of overlapping genes, showing the averaged expression of a gene across breast cancer cores profiled by the indicated panel, normalized to 100,000 vs the average FPKM from TCGA for all samples of a matched tissue type (BRCA). (b) Same as (a) but for lung cancer cores plotted vs averaged LUAD and LUSC samples from TCGA. (c) Same as (a) but showing breast cores vs averaged nTPM values from GTEx breast samples. (d) Same as (a) but for lung cores and samples. † denotes the MERSCOPE lung data acquired with a 5-µm imaging depth on FFPE sample. ‡ denotes the normal tissue TMA data of MERSCOPE which failed initial QC. (e) Heatmap of Z-scored average gene expression for several canonical marker genes in the indicated tissue cores for the Xenium multi-tissue panel (left) and CosMx 1K panel (right).

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques: Expressing, Imaging, Gene Expression, Marker

Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) Top row: DAPI image overlaid with cell segmentation boundaries (subset). Middle row: all the transcripts in green dots, white lines for the cell boundaries, and EPCAM in blue dots. Bottom row: segmented cell boundaries before and after filtration. (b) Violin plot of segmented cells per unit area before (left half) and after filtration (right half) grouped by panel with tumor and normal TMA data combined. (c) Same as (b) but showing cell areas before and after filtration. (d) Line plot showing remaining cells in percentage after filtering with various thresholds (transcripts per cell). Dotted lines indicate selected thresholds: 10 transcripts or above for Xenium and MERSCOPE and 20 for CosMx. (e) Heatmap of transcripts per cell after filtration. All available genes are considered here for each panel. MERSCOPE lung panel (5 µm) excluded from this heatmap. (f) Same as (e) but showing unique genes per cell. (g) Co-expression density map for three pairs of disjoint genes (rows) from all three platforms (columns). All cells across all tissues which include at least one detected transcript of either of the indicated genes are plotted together, with color indicating the number of cells at the indicated expression levels of each gene.

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques: Filtration, Expressing

Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) Heatmap of Z-scored gene expression showing CosMx’s ability to specifically identify known lineage markers. We focused on the normal tissue TMA profiled with multi-tissue panel and selected genes with canonical expression patterns for this analysis. (b) Same as (a) but for MERSCOPE (breast panel). (c) Heatmap of transcripts per cell after filtration. Only shared genes (40) are considered here for each panel. (d) Same as (c) but showing unique transcripts from the same gene set.

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques: Gene Expression, Expressing, Filtration

Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) Global Clustering results of tumor TMA from Xenium breast panel (top), Xenium lung panel (middle), and Xenium panhuman panel (bottom). (b) Global Clustering results of tumor TMA from MERFISH breast panel (top), MERSCOPE lung panel (middle), and CosMx multitissue panel (bottom). (c) Global Clustering results of normal TMA from Xenium breast panel (top), Xenium lung panel (middle), and Xenium panhuman panel (bottom). (d) Global Clustering results of normal TMA from MERSCOPE breast panel (top), MERSCOPE lung panel (middle), and CosMx multitissue panel (bottom).

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques:

Journal: bioRxiv

Article Title: Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues

doi: 10.1101/2023.12.07.570603

Figure Lengend Snippet: (a) To facilitate standardized data formatting and subsequent analytical processes, we built this data ingestion pipeline with the following objectives: 1) to grab cell-level and transcript-level data from diverse platforms and normalize the data structure; 2) to tag each cell and transcript with essential metadata including tissue type, tumor status, PD-L1 status, among others; and 3) to transform the data into various formats tailored to the requirements of particularized analyses. Specifically, to tag the data, core centers in the TMA were pinpointed using DAPI images (Xenium) or cell metadata that contains global coordinates (MERSCOPE and CosMx) using QGIS(version:3.16.10-Hannover). Cells or transcripts within a specified radius were then labeled with core metadata via spatial joining (implemented by GeoPandas, version:0.13.0). In instances where the cores are in close proximity or when a uniform radius cannot be applied effectively, we manually generated the core boundary masks.

Article Snippet: Three companies recently released the first FFPE compatible commercial iST platforms: 10X’s Xenium, Nanostring’s CosMx, and Vizgen’s MERSCOPE [ , , , ] .

Techniques: Labeling, Generated

Journal: bioRxiv

Article Title: MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

doi: 10.64898/2026.03.06.710199

Figure Lengend Snippet: Fresh frozen mouse brain sections were profiled with an 815-plex MERSCOPE Pan Neuro Panel and imaged on MERSCOPE platform to compare MERFISH 1.0 and MERFISH 2.0 chemistries. A) Sensitivity comparison between MERFISH (blue) and MERFISH 2.0 (red) measured as RNA transcript counts per 100 µm .Bars represent mean values across biological replicates (N=3). MERFISH 2.0 shows increased transcript detection and reduced variability relative to MERFISH 1.0. B ) Distribution of detected transcripts per cell for MERFISH 1.0 and MERFISH 2.0, shown as histograms of log10-transformed transcript counts per cell. MERFISH 2.0 exhibits higher transcript counts per cell. C ) UMAP visualization of major neuronal and non-neuronal cell populations identified using MERFISH 1.0 and MERFISH 2.0 data. The MERFISH 1.0 and MERFISH 2.0 data was combined for analysis and co-embedding in the UMAP. D) Relative abundance of annotated cell types detected with MERFISH 1.0 and MERFISH 2.0, shown as the percentage of total cells assigned to each cell type.

Article Snippet: MERFISH 1.0 sample preparation followed published protocols and manufacturer’s instructions: MERSCOPE Fresh and Fixed Frozen Tissue Sample Preparation User Guide (Vizgen PN 91600002) and MERSCOPE FFPE Tissue Sample Preparation User Guide (Vizgen PN 91600112).

Techniques: Comparison, Transformation Assay

Journal: bioRxiv

Article Title: MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

doi: 10.64898/2026.03.06.710199

Figure Lengend Snippet: Fresh-frozen human brain sections were profiled using the 815-plex MERSCOPE Human Brain Panel and imaged on the MERSCOPE platform to compare MERFISH 1.0 and MERFISH 2.0 chemistries. A) Comparison of transcript detection between MERFISH 1.0 and MERFISH 2.0 on adjacent tissue slices. Scatter plot shows transcript counts detected by the two chemistries across the panel. B) Distribution of detected transcripts per cell for MERFISH 1.0 and MERFISH 2.0 shown as histograms of log10-transformed transcript counts per cell. MERFISH 2.0 shows increased transcript detection per cell. C-D) Correlation between bulk RNA-seq and MERFISH data with MERFISH 1.0 (C) or MERFISH 2.0 (D), demonstrating strong concordance between spatial and bulk measurements. E-F) Spatial heat map of transcript/cell across the tissue section for MERFISH 1.0 (E) and MERFISH 2.0 (F) chemistry illustrating increased transcript detection with MERFISH 2.0. G) Violin plot showing transcripts counts per cell across representative cell types identified in the human brain, including glutamatergic neurons, GABAegeric neurons, oligodendrocytes, astrocytes, vascular cells, and microglia cells. MERFISH 2.0 exhibits a broader dynamic range of transcript detection across cell types. H) Spatial distribution of representative marker genes with MERFISH 1.0 (top) and 2.0 (bottom) chemistry, including OLIG2, MOG and SOX10 with DAPI staining marking nuclei. MERFISH 2.0 shows substantially increased transcript counts for each marker gene.

Article Snippet: MERFISH 1.0 sample preparation followed published protocols and manufacturer’s instructions: MERSCOPE Fresh and Fixed Frozen Tissue Sample Preparation User Guide (Vizgen PN 91600002) and MERSCOPE FFPE Tissue Sample Preparation User Guide (Vizgen PN 91600112).

Techniques: Comparison, Transformation Assay, RNA Sequencing, Marker, Staining

Journal: bioRxiv

Article Title: MERFISH 2.0, an ultra-sensitive single-cell spatial transcriptomics imaging chemistry across diverse tissue types

doi: 10.64898/2026.03.06.710199

Figure Lengend Snippet: Archival fresh-frozen human brain sections with reduced RNA quality were profiled using the 815-plex MERSCOPE Human Brain Panel and imaged on the MERSCOPE platform to compare MERFISH 1.0 and MERFISH 2.0 chemistries. A) Sensitivity comparison between MERFISH 1.0 (blue) or MERFISH 2.0 (red), measured as RNA transcript counts per 100 µm². Bars represent mean values across biological replicates (n = 3). MERFISH 2.0 shows substantially increased transcript detection. B) Distribution of detected transcripts per cell for MERFISH 1.0 and MERFISH 2.0, shown as histograms of log10-transformed transcript counts per cell, demonstrating increased transcript detection with MERFISH 2.0. C) UMAP visualization of different cell types identified in human brain with MERFISH 1.0, with 10,463 cells pass QC. Left: clustering of cell types based on gene expression profiles. Right: spatial distribution of annotated cell types across the tissue section. D) UMAP visualization of cell populations identified in human brain with MERFISH 2.0, with 21,236 cells pass QC. Left: clustering of cell types. Right: spatial distribution of annotated cell types. MERFISH 2.0 recovers substantially more cells and improves detection of distinct cell populations. E) Absolute number of cells assigned to each cell-type cluster with MERFISH 1.0 and MERFISH 2.0 chemistry. F) Relative abundance of cell types detected with MERFISH 1.0 and MERFISH 2.0 chemistry, shown as the percentage of total cells assigned to each cluster. MERFISH 2.0 identifies a higher fraction of astrocytes and uniquely detects MGE interneurons that are not recovered with MERFISH 1.0.

Article Snippet: MERFISH 1.0 sample preparation followed published protocols and manufacturer’s instructions: MERSCOPE Fresh and Fixed Frozen Tissue Sample Preparation User Guide (Vizgen PN 91600002) and MERSCOPE FFPE Tissue Sample Preparation User Guide (Vizgen PN 91600112).

Techniques: Comparison, Transformation Assay, Gene Expression

Journal: Neuropsychopharmacology

Article Title: Targeting GPR3 as a novel approach for nicotine cessation therapeutic development

doi: 10.1038/s41386-025-02202-3

Figure Lengend Snippet: a GPR3 is expressed in cholinergic neurons of the ventral medial habenula. Top left panel: Representative image of coronal mouse brain slice, with the medial habenula outlined in green. Top middle panel: MERSCOPE image of medial habenula displaying ChAT (red) and GPR3 (green) transcripts. Scale bar = 500 μm. Top right panel: Quantification of GPR3 cells co-expressing ChAT from Vizgen’s publicly available MERSCOPE datasets (n = 3 female mice, 6–8 weeks of age) reveals that the majority of the GPR3 positive cells co-localize with ChAT. Bottom panels I, II and III: Higher magnification images of the denoted areas I, II and III from the white square outlines in the top middle panel. Cells shown express GPR3 transcripts (green), ChAT transcripts (red) and DAPI (blue). White arrows denote the GPR3 mRNA puncta. Scale bar = 10 μm. b – g Reduced nicotine self-administration following administration of the GPR3 agonist, RTI-19318-32, in mice. b At the low dose of self-administered nicotine (0.03 mg/kg/infusion; n = 7 male mice), both the 1 and 10 mg/kg doses of RTI-19318-32 significantly decreased nicotine intake. Graph shows both the number of nicotine infusions earned (left y-axis) and total mg/kg nicotine consumed (right y-axis). c Active lever pressing was selectively reduced with administration of the 10 mg/kg dose of RTI-19318-32, and no differences were found with inactive lever pressing. d At the moderate dose of self-administered nicotine (0.1 mg/kg/infusion; n = 7 male mice), administration of the 1 and 10 mg/kg doses of RTI-19318-32 significantly decreased nicotine intake. The graph shows both the number of nicotine infusions earned (left y-axis) and total mg/kg nicotine consumed (right y-axis). e Active lever pressing was selectively reduced at both the 1 and 10 mg/kg RTI-19318-32 doses, with no differences for inactive lever pressing behavior. f At the high dose of self-administered nicotine (0.25 mg/kg/infusion; n = 7 male mice), significant reductions in the number of nicotine infusions earned were found for both the 1 and 10 mg/kg RTI-19318-32 doses. The number of nicotine infusions earned (left y-axis) and total mg/kg nicotine consumed (right y-axis) are shown. g RTI-19318-32 selectively reduced lever pressing behavior at the active, but not at the inactive lever. Data represented as mean ± SEM; all individual data points shown on bar figures. *p < 0.05, ***p < 0.001, ****p < 0.0001.

Article Snippet: MERSCOPE images and co-localization quantification was conducted through the publicly available dataset, Vizgen MERFISH Mouse Receptor Map ( https://info.vizgen.com/mouse-brain-map ).

Techniques: Slice Preparation, Expressing

Journal: medRxiv

Article Title: A network-based atlas of human skeletal muscle aging

doi: 10.64898/2026.02.15.26346348

Figure Lengend Snippet: A) Fibre type specific gene expression in agreement with Murgia et al 2021. B) Using GeoMX we find a number of genes are differentially regulated in Type I vs Type II fibres, with atrophy – this includes three network module genes, GDNF-SVIL-RBFOX1 C) Merscope profiles before and after human muscle unloading. GDNF (yellow) expression in four ROIs (before and after 2 weeks of disuse). Mature muscle nuclei (MYREM+; blue) muscle satellite cells (MEG3/PAX7+;green) and endothelial cells (APLNR+/ENG+/KDR+/TIE1+; pink). At low magnification fast (ATP2A1, green) and slow muscle (MYH7, blue) fibres are stained. At higher magnification, fast are unstained (ATP2A1 fish channel switched off) and slow fibres are blue (MYH7). Clear examples of GDNF expression in or around mature skeletal muscle nuclei (MYREM+; blue) are show with 4-10 times more GDNF after unloading and consistent with the bulk analyses (Supplemental Table S7)

Article Snippet: Briefly, each fresh frozen sample embedded in the optimal cutting temperature compound (OCT, Tissue-Tek, The Netherlands) was sectioned at a thickness of 10 μm in a cryostat at -20 °C and transferred onto the circular MERSCOPE glass slide (PN 2040001, Vizgen, USA) within the fiducial bead border, and allowed to adhere to the glass for 5 minutes 77,182 .

Techniques: Gene Expression, Expressing, Staining

Journal: medRxiv

Article Title: A network-based atlas of human skeletal muscle aging

doi: 10.64898/2026.02.15.26346348

Figure Lengend Snippet: Merscope ROI QC Data

Article Snippet: Briefly, each fresh frozen sample embedded in the optimal cutting temperature compound (OCT, Tissue-Tek, The Netherlands) was sectioned at a thickness of 10 μm in a cryostat at -20 °C and transferred onto the circular MERSCOPE glass slide (PN 2040001, Vizgen, USA) within the fiducial bead border, and allowed to adhere to the glass for 5 minutes 77,182 .

Techniques:

Journal: medRxiv

Article Title: A network-based atlas of human skeletal muscle aging

doi: 10.64898/2026.02.15.26346348

Figure Lengend Snippet: Using Merscope merfish assays we show rare examples of IL6 (yellow) as well as IL6 receptors (red) in four ROIs (with and without muscle use) from samples with the highest total IL6 count out of 54 examples. A ) Fast (unstained) and slow fibres (MYH7, blue). Mature muscle nuclei (MYREM+; blue) muscle satellite cells (MEG3/PAX7+;green) and endothelial cells (APLNR+/ENG+/KDR+/TIE1+; pink). Overall IL6 is not reliably expressed in human muscle fibres with a single molecule detected in fewer than 1/10 th of fibres, a level we cannot distinguish from indirect contamination/background. B ) In stark contrast, we find isolated examples of numerous IL6 mRNA inside endothelial cells in certain biopsy samples (young healthy muscle). These IL6 expressing endothelial cells are rare so they also cannot be the main source of robust IL6 is qPCR experiments using whole biopsy cDNA libraries – which probably reflects immune cells in the biopsy and these are presumably more abundant in post-exercise tissue due to the increased blood perfusion.

Article Snippet: Briefly, each fresh frozen sample embedded in the optimal cutting temperature compound (OCT, Tissue-Tek, The Netherlands) was sectioned at a thickness of 10 μm in a cryostat at -20 °C and transferred onto the circular MERSCOPE glass slide (PN 2040001, Vizgen, USA) within the fiducial bead border, and allowed to adhere to the glass for 5 minutes 77,182 .

Techniques: Isolation, Expressing

Journal: medRxiv

Article Title: A network-based atlas of human skeletal muscle aging

doi: 10.64898/2026.02.15.26346348

Figure Lengend Snippet: Using the Xenium spatial platform and a 460-plex gene assay (a subset of the Merscope v1 chemistry 960-plex assay) we measure IL6 (yellow) in human muscle. Endothelial cells show specific APLNR, ENG and TIE1 expression (Pink), muscle satellite Cell show MEG3 and PAX7 expression (Green) while mature muscle nuclei expression the noncoding RNA MYREM (Blue). Nuclei are stained with DAPI (show in white as is the cell membrane). Using this second immunofluorescence spatial technology we find no evidence that IL6 is robustly expressed in human muscle cells – with a single IL6 mRNA molecule in one in every ∼20 cells. We cannot rule out these few being non-specific contamination from other cell types. Given the typical signal found using qPCR and cDNA derived from a 20mg tissue biopsy we conclude that IL6 gene expression in muscle tissue is probably derived from immune cells and therefore it is not a myokine.

Article Snippet: Briefly, each fresh frozen sample embedded in the optimal cutting temperature compound (OCT, Tissue-Tek, The Netherlands) was sectioned at a thickness of 10 μm in a cryostat at -20 °C and transferred onto the circular MERSCOPE glass slide (PN 2040001, Vizgen, USA) within the fiducial bead border, and allowed to adhere to the glass for 5 minutes 77,182 .

Techniques: Gene Assay, Plex Assay, Expressing, Staining, Membrane, Immunofluorescence, Derivative Assay, Gene Expression

Journal: medRxiv

Article Title: A network-based atlas of human skeletal muscle aging

doi: 10.64898/2026.02.15.26346348

Figure Lengend Snippet: Using FISH probes for the three main fibres types, we illustrate the variation in Type II hybrid types we observed using the Merscope technology. This clarifies that Type IIx gene expression is found in human muscle

Article Snippet: Briefly, each fresh frozen sample embedded in the optimal cutting temperature compound (OCT, Tissue-Tek, The Netherlands) was sectioned at a thickness of 10 μm in a cryostat at -20 °C and transferred onto the circular MERSCOPE glass slide (PN 2040001, Vizgen, USA) within the fiducial bead border, and allowed to adhere to the glass for 5 minutes 77,182 .

Techniques: Gene Expression

Journal: medRxiv

Article Title: A network-based atlas of human skeletal muscle aging

doi: 10.64898/2026.02.15.26346348

Figure Lengend Snippet: Using the Xenium spatial platform and a 460-plex gene assay (a subset of the Merscope v1 chemistry 960-plex assay) we confirm that some classic cytosolic fibre type specific markers are unsuitable to classify single-nuclei profiles (e.g. MYH7). While MYH7 is, for example, specific to Type I muscle fibres in the cytoplasm, lineage tracing and the present data demonstrate that human muscle nuclei don’t express such genes in a fibre-type specific gene expression pattern and thus can not be utilized to assign snRNAseq profiles to individual fibres types. Only spatial single cell technologies can reliably assign molecular profiles to specific cell types

Article Snippet: Briefly, each fresh frozen sample embedded in the optimal cutting temperature compound (OCT, Tissue-Tek, The Netherlands) was sectioned at a thickness of 10 μm in a cryostat at -20 °C and transferred onto the circular MERSCOPE glass slide (PN 2040001, Vizgen, USA) within the fiducial bead border, and allowed to adhere to the glass for 5 minutes 77,182 .

Techniques: Gene Assay, Plex Assay, Gene Expression, Single Cell