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

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