Data for Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq

Author ORCID

Tabea Soelter 0000-0003-1654-4240

Timothy C. Howton 0000-0002-9423-0135

Amanda D. Clark 0000-0002-1186-3114

Vishal H. Oza 0000-0001-6990-0267

Brittany Lasseigne 0000-0002-1642-8904

Publication Date

11-28-2023

Abstract

data.tar.gz contains all files from the data directory associated with the 230313_TS_CCCinHumanAD GitHub project and includes the following:

  • CellRangerCounts/
    • GSE157827/
      • post_soupX/ : contains 21 directories for 21 samples, which each contain 3 files obtained from ambient RNA removal with soupX. Below is a representative example, but this repo contains 1 directory per sample:
        • SAMN16100290_S01_AD/
          • barcodes.tsv
          • genes.tsv
          • matrix.mtx
      • pre_soupX/ : contains 21 directories for 21 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 repo contains 1 directory per sample:
        • SAMN16100290_S01_AD/
          • filtered_feature_ bc_matrix.h5
          • Raw_feature_bc_matrix.h5
    • GSE174367/ : contains 19 directories for 19 samples, which contain 3 files each from Cell Ranger alignment of fastq files to the reference genome. Below is a representative example, but this repo contains 1 directory per sample:
      • SAMN19128610_S1_CTRL/
        • barcodes.tsv
        • genes.tsv
        • Matrix.mtx
  • ccc/
    • nichenet_grn/
      • gr_network_human_21122021.rds : accessed in October 2023, gene regulation network – gene regulatory information from MultiNicheNet
      • ligand_tf_matrix_nsga2r_final.rds: accessed in October 2023, ligand tf matrix for signaling path determination from MultiNicheNet
      • signaling_network_human_21122021.rds : accessed in October 2023, signaling network – protein-protein interaction information from MultiNicheNet
      • weighted_networks_nsga2r_final.rds : accessed in October 2023, networks weighted by literature evidence from MultiNicheNet
    • nichenet_prior/
      • ligand_target_matrix.rds : accessed in April 2023, ligand to target matrix from NicheNet
      • lr_network.rds : accessed in April 2023, ligand-receptor matrix from NicheNet
    • nichenet_v2_prior/
      • ligand_target_matrix_nsga2r_final.rds : accessed in June 2023, ligand to target matrix from MultiNicheNet used to predict target genes.
      • lr_network_human_21122021.rds : accessed in June 2023, ligand-receptor matrix from MultiNicheNet used to predict ligand-receptor pairs.
    • geo_multinichenet_output.rds : MultiNicheNet output for Morabito et al., 2021 data
    • geo_signaling_igraph_objects.rds : list of igraph objects for 17 overlapping LRTs and their signaling mediators in the Morabito et al., 2021 dataset.
    • gse_multinichenet_output.rds : MultiNicheNet output for Lau et al., 2020 data
    • gse_signaling_igraph_objects.rds : list of igraph objects for 17 overlapping LRTs and their signaling mediators in the Lau et al., 2020 dataset
  • seurat_preprocessing/
    • geo_filtered_seurat.rds : merged and filtered seurat object of Morabito et al., 2021 data
    • geo_integrated_seurat.rds : seurat object integrated using harmony of Morabito et al., 2021 data
    • geo_clustered_seurat.rds : clustered seurat object of Morabito et al., 2021 data
    • geo_processed_seurat.rds : processed seurat object with final cell type assignments at specified resolution of Morabito et al., 2021 data
    • gse_filtered_seurat.rds : merged and filtered seurat object of Lau et al., 2020 data
    • gse_integrated_seurat.rds : seurat object integrated using harmony of Lau et al., 2020 data
    • gse_clustered_seurat.rds : clustered seurat object of Lau et al., 2020 data
    • gse_processed_seurat.rds : processed seurat object with final cell type assignments at specified resolution of Lau et al., 2020 data

Keywords

Alzheimer's disease, neurodegeneration, cell-cell communication, signaling, single-cell, networks, genomics

Repository

Zenodo

Distribution License

The MIT License

Link to Dataset

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