MERFISH

The Vizgen MERFISH Mouse Liver Map dataset contains a MERFISH measurement of a 347 gene panel. The dataset includes detected transcripts, gene counts per cell, cell spatial metadata, cell boundaries, and DAPI images

MERFISH, which stands for Multiplexed Error-Robust Fluorescence In Situ Hybridization, is a cutting-edge technology that revolutionizes the field of spatial transcriptomics. It allows researchers to map and quantify the expression levels of hundreds to tens of thousands of RNA molecules within individual cells, while also maintaining their precise locations within a tissue sample. This provides a much deeper understanding of how gene expression is organized and regulated in tissues, compared to traditional bulk RNA sequencing methods which average over all cells in a sample and lose spatial information

Note: Data used here for analysis was acquired from publicly available at Vizgen website

Figure: Visualization of Vizgen single-cell gene expression data (A) spatial location in the mouse liver tissue (B) dimensionality reduced UMAP embedding (C) colored using their Leiden cluster (D) Specific gene expression on spatial (left), UMAP cluster (center), liver zonation expression profile in mouse liver.

The benefits of using MERFISH are numerous:

• High Multiplexing Capacity:

MERFISH can measure the expression of thousands of genes simultaneously, providing a much more comprehensive picture of cellular activity.

• Single-Cell Resolution:

Unlike bulk RNA sequencing, MERFISH preserves the spatial context of gene expression, allowing researchers to see which genes are active in specific cell types and locations within a tissue.

• Quantitative Measurements:

MERFISH provides accurate counts of individual RNA molecules, enabling researchers to precisely measure gene expression levels.

• Versatility:

MERFISH can be used to study a wide variety of tissues and cell types, making it a powerful tool for research in many areas of biology and medicine.

The figure shown below titled "MERFISH" illustrates the interplay between fibroblasts, COL1A1, and CXCL1 in the tumor microenvironment (TME). It shows how COL1A1 activates cancer-associated fibroblasts (CAF) and induces CXCL1 secretion in tumor cells. The panels depict:

COL1A1 and Fibroblast Interaction: Highlighting the activation of fibroblasts by COL1A1.
CAF and CXCL1: Showing areas where CAFs and CXCL1 are present.
COL1A1 and Fibroblast: Another view of the interaction with a different color scheme.
CXCL1 Secretion: Comparing CXCL1 secretion from tumor cells and CAFs.

This research underscores the complexity of TME and the significant role of COL1A1 in activating CAFs and promoting CXCL1 secretion, which contributes to tumor progression. The MERFISH analysis of CRC cancer TME is crucial for capturing cytokine cellular communication, providing insights into the spatial organization and interactions of cells within the tumor microenvironment.

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