CosMx Spatial Transcriptomics Dataset of Human Lung Explants (Uninfected vs. Alpha Strain)

This dataset contains CosMx spatial transcriptomics data derived from human lung explants from a single patient, focusing on comparisons between uninfected samples and samples infected with the Alpha variant of SARS-CoV-2. The dataset contains transcript detections for 1000 genes across multiple fields-of-view (FOVs).

Files included:

1. Casp8_genes.csv
   Contains the list of 42 prioritized genes categorized into four groups. 

2. CosMx_hlc_total_detection_per_fov_patient1.csv
   Provides total gene detections per FOV for the uninfected and Alpha strain samples from patient 1. Used for normalization purposes.

3. CosMx_hlc_Uninfected_Alpha_patient1_transcript.csv
   Raw transcript detection for each gene within individual FOVs, separately indicated for uninfected and Alpha strain samples. These data were normalized to account for differences in sequencing depth across FOVs.

4. casp8_CosMx_hlc_heatmap.R
   R script used to generate heatmaps of normalized gene expression data using the ComplexHeatmap package (version 2.24.0) in R (version 4.5.0). It includes normalization steps and visualization code.