merscope verification kit  (Vizgen Inc)

Journal: bioRxiv

Article Title: High resolution spatial profiling of the hematopoietic landscape of the murine lung

doi: 10.1101/2025.09.25.678618

Figure Lengend Snippet: A) This figure shows the scRNA CellRef data (colored) projected on top of our MERSCOPE data (grey) and how they align. B) The UMAP after subsequent label application onto our samples, improving the resolution of our calls and allowing for the identification of nearly 40 discrete cell types across our data sets.

Article Snippet: Sample quality was further validated using the MERSCOPE Sample Verification Kit (Vizgen, Cat. 10400008) with probes targeting the mouse housekeeping gene Eef2 in a rapid imaging protocol in laser channels 561 and 647.

Techniques:

Journal: bioRxiv

Article Title: High resolution spatial profiling of the hematopoietic landscape of the murine lung

doi: 10.1101/2025.09.25.678618

Figure Lengend Snippet: A) A dot plot showing relative enrichment and depletion of 11 representative types of ligand/receptor signaling between cell types within our samples, derived from a table of spatial cell-cell communication scores. The size of the dots reflects the significance, while the color represents relative fold change of observed interactions compared to a hypothetical null distribution over 1000 iterations. B) An overview of a subsection of tissue from sample B, displaying representative zoomed views of several types of L/R signaling, showcasing the capabilities of MERSCOPE to resolve each respective transcript at sub-cellular resolution. (C) Bmp4–Bmpr2 (BMP signaling): Bmpr2 receptors (white) were abundant in CAP2 endothelial, AT1/AT2 epithelial, pericytes, and venous endothelial cells, while Bmp4 ligands (yellow) were less frequent but present in AT1/AT2, AF2 fibroblasts, ILCs, and ciliated cells. Occasional junctions, such as AF2–epithelial boundaries, demonstrated potential stromal-to-epithelial signaling. (D) Vegfa–Flt1 (angiogenesis): Vegfa ligands (red) were observed around ciliated/deuterosomal cells and within AT1/AT2 epithelium, fibroblasts (AF1/AF2), mesothelial cells, and CAP1/EPC endothelium. Flt1 receptors (green) were most prominent in AT1/AT2 and AF2 fibroblasts, with additional expression in mesothelial and endothelial subsets. Ligand and receptor co-localization in AT1/AT2 and AF2 suggests autocrine signaling, while complementary expression at epithelial–endothelial junctions supports paracrine communication. (E) Col1a1–Itga1 (matrix–integrin interactions): Col1a1 ligands (pink) were abundant in AF2 fibroblasts, SCMFs, and immune subsets (ILCs, cDC1, cDC2), whereas Itga1 receptors (orange) localized mainly to pericytes, VSMCs, and AT1/AT2 epithelium. Overlaps occurred at fibroblast–immune and epithelial–pericyte interfaces, suggesting collagen-mediated matrix–integrin signaling across stromal–epithelial and stromal–vascular boundaries. Together, these images highlight spatially resolved ligand–receptor cross-talk across stromal, epithelial, endothelial, and immune compartments of the lung.

Article Snippet: Sample quality was further validated using the MERSCOPE Sample Verification Kit (Vizgen, Cat. 10400008) with probes targeting the mouse housekeeping gene Eef2 in a rapid imaging protocol in laser channels 561 and 647.

Techniques: Derivative Assay, Expressing