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

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