Analysis, Supplementary, and Image files for Spatiotemporal study with Norway spruce

Phylotrees_data_alignment folder contains alignment results for CYP, MADSbox and YABBY gene families. STdeconvolve contains the seurat objects and main output tables (in excel format) from the analysis performed using STdeconvolve for the different budtype-timepoint groups (Acrocona October, Seed cone/Female October, and Vegetative October). The beta matrices correspond to gene expression profile for each deconvolved cell type, and the theta matrices correspond to cell type proportion per spot.

There is one beta matrix + one theta matrix for each bud type. In addition, the folder contains marker gene table for every cell type (Supplemental_Table_STDeconvolve_markers.xlsx) and Gene Ontology Biological Process terms for each STdeconvolve cell type (Supplemental_Table_STdeconvolve_GO.xlsx). Trajectory_analysis_objects folder contains the the seurat objects (LOAcro.merged.PCA.harmony_2024-11-03.rds and LOFem.merged.PCA.harmony_2024-11-03.rds) and the marker genes from the subclustering (Supplemental_Table_subclustering_markers.xlsx) from the Pseudotime analysis. hdWGCNA folder contains spatial heatmaps for modules 2 and 7 in all the tissue sections in acrocona transition shoot primordia and seed cone primordia and the module marker table for each of the modules (Supplemental_Table_moduleMarkers.xlsx).

The file Brightfield_images_spruce.zip contains the microscopy images in their original size that can be used for plotting purposes and for other image analysis. RT-qPCR raw data for YABBY gene analysis is also placed here as an excel document (qPCR_spruceData_submission.xlsx).