DOI: 10.5281/zenodo.11043320
title: Data for Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points

description: 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