2026-10-14T08:25:35Z https://data.mendeley.com/oai

oai:data.mendeley.com/b7fppw63v8.2 2026-09-09T07:13:38Z

Masarapu, Yuvarani Analysis, Supplementary, and Image files for Spatiotemporal study with Norway spruce Mendeley Data This dataset contains the files needed to reproduce the spatial data analysis in the study titled 'Norway spruce spatiotemporal programs of conifer reproductive development'. Bract vs. Ovuliferous scales folder contains the differentially expressed genes between manually selected bract and ovuliferous scale pairs from September and October seed cone primordia. Clustering/Spruce_HE_images.zip contains the low resolution images needed to reproduce the spatial data clustering analysis. For the same analysis, spot alignment files are required containing the spots information for each bud section. We have 88 files here, each corresponding to each bud tissue section. The seurat object from the clustering analysis is saved as Clustering/spruce_merged_PCA_harmony_Umap_FindNeigh_findClusters.rds DAP-seq folder contains the concensus peaks from the analysis (SPL1.consensus_peaks.narrowPeak.gz) and motif files for the performed two replicates (SPL1_1_meme-chip.html, SPL1_2_meme-chip.html). 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). Evolutionary Biology Developmental Biology Conifer Picea RNA Sequencing Spatial Analysis Real-Time Polymerase Chain Reaction Plant Bioinformatics Agriculture Industry Plant Development Spatial Transcriptomics Phylogenetic Analysis Saarenpää, Sami Dataset doi:10.17632/b7fppw63v8.2 oai:data.mendeley.com/b7fppw63v8.2 Creative Commons Attribution 4.0 International http://creativecommons.org/licenses/by/4.0 https://data.mendeley.com/datasets/b7fppw63v8 2026-09-09T07:13:38Z