AI Article Synopsis
- Single cell RNA sequencing (scRNAseq) is changing how we study gene expression, but it often only shows the differences between cell types in a basic 2D plot.
- The new method, called vSPACE, creates a virtual spatial map of scRNAseq data from human articular cartilage, mimicking spatial transcriptomics.
- This approach reveals consistent zonal distribution patterns in gene expression across various healthy donors, indicating reliable insights despite differences in age and sex.
Article Abstract
Single cell RNA sequencing technology has been dramatically changing how gene expression studies are performed. However, its use has been limited to identifying subtypes of cells by comparing cells' gene expression levels in an unbiased manner to produce a 2D plot (e.g., UMAP/tSNE). We developed a new method of placing cells in 2D space. This system, called vSPACE, shows a virtual spatial representation of scRNAseq data obtained from human articular cartilage by emulating the concept of spatial transcriptomics technology, but virtually. This virtual 2D plot presentation of human articular cartage cells generates several zonal distribution patterns, in one or multiple genes at a time, reveling patterns that scientists can appreciate as imputed spatial distribution patterns along the zonal axis. The discovered patterns are explainable and remarkably consistent across all six healthy doners despite their respectively different clinical variables (age and sex), suggesting the confidence of the discovered patterns.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10871300 | PMC |
| http://dx.doi.org/10.1101/2024.02.07.577817 | DOI Listing |
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