Visium spatial RNA-seq dataset reanalysis Script

To confirm expression of genes within human nociceptors, we performed a reanalysis of a visum spatial transcriptome available at http://sensoryomics.com/(opens in new window) (10.1126/scitranslmed.abj8186) for gene expression analysis.

To view the data, the open-source software R version 4.4.1 is required, along with the packages: "Seurat" v.5.0.2 and "Tidyverse" v.2. The workflow is: The count matrices obtained from the Sensoryomics repository (http://sensoryomics.com/(opens in new window)) were processed and analyzed using the R package “Seurat”, v.5.0.2. For quality control, seurat objects were created for each sample, and a filter was applied to remove cells with counts below 2,000 genes and those lacking the neuronal marker SNAP25. After this step, the objects were combined and normalized using the variance stabilizing transformation (vst) method. For data integration, anchors were selected and the seurat objects were integrated using the canonical correspondence analysis (CCA) method implemented in the seurat algorithm. Clusters were identified using the PCA method and visualized through UMAP.

Access information

Data was derived from the following sources:

• Sensoryomics repository (http://sensoryomics.com/(opens in new window)), under creative commons licence Sensoryomics 2021.