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

Author ORCID

Tabea M. Soelter 0000-0003-1654-4240

Timothy C. Howton 0000-0002-9423-0135

Elizabeth J. Wilk 0000-0002-7078-1215

Jordan H. Whitlock 0000-0002-9336-545X

Amanda D. Clark 0000-0002-1186-3114

Allison Birnbaum 0000-0002-8904-3917

Dalton C. Patterson 0000-0002-0208-7301

Constanza J. Cortes 0000-0002-6033-7428

Brittany N. Lasseigne 0000-0002-1642-8904

Publication Date

4-22-2024

Abstract

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

Repository

Zenodo

Distribution License

The MIT License

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