Data for Evaluation of altered cell-cell communication between glia and neurons in the hippocampus of 3xTg-AD mice at two time points
DOI10.5281/zenodo.11043321Zenodo11043321MaRDI QIDQ6694916FDOQ6694916
Dataset published at Zenodo repository.
Timothy C. Howton, Jordan H. Whitlock, Constanza J. Cortes, Dalton C. Patterson, Allison Birnbaum, Brittany N. Lasseigne, Amanda D. Clark, Elizabeth J. Wilk, Tabea M. Soelter
Publication date: 22 April 2024
Copyright license: MIT license
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
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