Data for Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points (Q6694916)

processed_data.tar.gz contains all files from the data directory associated with the 230418_TS_AgingCCC GitHub project and includes the following: CellRangerCounts/ post_soupX/ : contains 12 directories for 12 samples, which each contain 3 files obtained from ambient RNA removal with soupX. Below is a representative example, but the post_soupX directory contains one directory for each of the 12 samples: S01_6m_AD/ barcodes.tsv genes.tsv matrix.mtx pre_soupX/ : contains 12 directories for 12 samples, which each contain 2 files obtained from Cell Ranger after aligning fastq files to the reference genome. Below is a representative example, but this directory contains 1 directory for each individual sample: S01_6m_AD/outs/ filtered_feature_ bc_matrix.h5 raw_feature_bc_matrix.h5 PANDA_inputs/ PANDA_exp_files_array.txt: Text files with files paths to expression inputs for PANDA gene regulatory networks. mm10_TFmotifs.txt: Mouse TF motif input for PANDA gene regulatory networks. Previously published in Whitlock et al. 2023 mm10_ppi.txt: Mouse protein-protein interaction information from SringDB input for PANDA gene regulatory networks. Previously published in Whitlock et al. 2023 ccc/ nichenet_v2_prior/ gr_network_mouse_21122021.rds : accessed in December 2023, gene regulation network gene regulatory information from MultiNicheNet ligand_target_matrix_nsga2r_final_mouse.rds: accessed in December 2023, ligand target matrix for mouse from MultiNicheNet. ligand_tf_matrix_nsga2r_final_mouse.rds: accessed in December 2023, mouse ligand tf matrix for signaling path determination from MultiNicheNet lr_network_mouse_21122021.rds : accessed in December 2023, ligand-receptor matrix from MultiNicheNet signaling_network_mouse_21122021.rds : accessed in December 2023, signaling network protein-protein interaction information from MultiNicheNet for mouse weighted_networks_nsga2r_final_mouse.rds : accessed in October 2023, networks weighted by literature evidence from MultiNicheNet for mouse multinichenet_output.rds : MultiNicheNet output for 3xTg-AD snRNA-seq data 12m_signaling_igraph_objects.rds : list of igraph objects for 93 LRTs and their signaling mediators at 12 months 6m_signaling_igraph_objects.rds :list of igraph objects for 2 LRTs and their signaling mediators at 6 months elisa/: CSV files of measured OD values for every ELISA. 240319_ELISA_Ab40.csv: OD measurements for Ab40 240319_ELISA_Ab42.csv: OD measurements for Ab42 240319_ELISA_total_tau.csv: OD measurements for Total Tau panda/: PANDA gene regulatory networks for each time point and condition in excitatory and inhibitory neurons. Used for differential gene targeting. excitatory_neurons_AD12.Rdata excitatory_neurons_AD6.Rdata excitatory_neurons_WT12.Rdata excitatory_neurons_WT6.Rdata inhibitory_neurons_AD12.Rdata inhibitory_neurons_AD6.Rdata inhibitory_neurons_WT12.Rdata inhibitory_neurons_WT6.Rdata pseudobulk/: includes pseudo bulk matrices for every cell type which were used for downstream analyses. Each matrix also includes metadata information on condition and time point. all_counts_ls.rds: List of all the pseudo bulk matrices (below). astrocytes.rds: pseudobulk matrix for astrocytes. Include time point and condition information for downstream analyses. endothelial_cells.rds: pseudobulk matrix for endothelial cells. Include time point and condition information for downstream analyses. ependymal_cells.rds: pseudobulk matrix for ependymal cells. Include time point and condition information for downstream analyses. excitatory_neurons.rds: pseudobulk matrix for excitatory neurons. Include time point and condition information for downstream analyses. fibroblasts.rds: pseudobulk matrix for fibroblasts. Include time point and condition information for downstream analyses. inhibitory_neurons.rds: pseudobulk matrix for inhibitory neurons. Include time point and condition information for downstream analyses. meningeal_cells.rds: pseudobulk matrix for meningeal cells. Include time point and condition information for downstream analyses. microglia.rds: pseudobulk matrix for microglia. Include time point and condition information for downstream analyses. oligodendrocytes.rds: pseudobulk matrix for oligodendrocytes. Include time point and condition information for downstream analyses. opcs.rds: pseudobulk matrix for oligodendrocyte progenitor cells. Include time point and condition information for downstream analyses. percicytes.rds: pseudobulk matrix for pericytes. Include time point and condition information for downstream analyses. rgcs.rds: pseudobulk matrix for retinal ganglion cells. Include time point and condition information for downstream analyses. pseudobulk_split/: Includes pseudo bulk count matrices split by time point and condition. Used for input to PANDA for gene regulatory network construction. excitatory_neurons_AD12.Rdata excitatory_neurons_AD6.Rdata excitatory_neurons_WT12.Rdata excitatory_neurons_WT6.Rdata inhibitory_neurons_AD12.Rdata inhibitory_neurons_AD6.Rdata inhibitory_neurons_WT12.Rdata inhibitory_neurons_WT6.Rdata seurat_preprocessing/ filtered_seurat.rds : merged and filtered seurat object integrated_seurat.rds : seurat object integrated using harmony clustered_seurat.rds : clustered seurat object processed_seurat.rds : processed seurat object with final cell type assignments at specified resolution Raw data publicly available on GEO under series accession: GSE261596