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