Spatial Transcriptomic Analysis of Focal and Normal Areas of Myocyte Disarray in Human Hypertrophic Cardiomyopathy
by Jason Laird 1, Gayani Perera 2, Rebecca Batorsky 3, Hongjie Wang 3, Knarik Arkun 4 and Michael T. Chin 2*
- Research Technology, Tufts University, Medford, MA 02144, USA
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
- Data Intensive Studies Center, Tufts University, Medford, MA 02155, USA
- Department of Pathology, Tufts Medical Center, Boston, MA 02111, USA
* Author to whom correspondence should be addressed.
Code used in the analysis of Hypertrophic Cardiomyopathy Spatial Transcriptomic Data (https://doi.org/10.3390/ijms241612625)
scripts/01_geomx_preprocessing.R
: GeoMx pre-processing (probe, segment, Gene QC, etc.)scripts/02_differential_expression.R
: Mixed model differential dxpression, volcano plots of DEGs, top DEGs for comparisons of interest, ROI distributionscripts/03_deg_enrichment.R
: Gene ontology enrichment of significant DEGs, dot plot of enriched terms, module expression plotsscripts/04_ligand_receptor.R
: Ligand receptor analysis, CellChat DB pathwaysscripts/05_deconvolution.R
: Deconvolution using matched snRNA-seq data and overlapping cell type markers, bar plot of cell type proportions, dot plot of cell type proportions, scatterplot of cell type diversity statisticscripts/06_supplemental.R
: Supplemental figures, overlap of significant DEGs between all comparisons, overall gene ontology enrichment dotplot, UMAP plot of snRNA-seq cell types, expresison of overlapping marker genes, supplemental table creation