Data for Altered Glia-Neuron Communication in Alzheimer's Disease Affects WNT, p53, and NFkB Signaling Determined by snRNA-seq
DOI10.5281/zenodo.10214497Zenodo10214497MaRDI QIDQ6694908FDOQ6694908
Dataset published at Zenodo repository.
Vishal H. Oza, Timothy C. Howton, Brittany N. Lasseigne, Tabea M. Soelter, Amanda D. Clark
Publication date: 28 November 2023
Copyright license: MIT license
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.tsvgenes.tsvmatrix.mtxpre_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.h5Raw_feature_bc_matrix.h5GSE174367/ : 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.tsvgenes.tsvMatrix.mtxccc/nichenet_grn/gr_network_human_21122021.rds : accessed in October 2023, gene regulation network – gene regulatory information from MultiNicheNetligand_tf_matrix_nsga2r_final.rds: accessed in October 2023, ligand tf matrix for signaling path determination from MultiNicheNetsignaling_network_human_21122021.rds : accessed in October 2023, signaling network – protein-protein interaction information from MultiNicheNetweighted_networks_nsga2r_final.rds : accessed in October 2023, networks weighted by literature evidence from MultiNicheNetnichenet_prior/ligand_target_matrix.rds : accessed in April 2023, ligand to target matrix from NicheNetlr_network.rds : accessed in April 2023, ligand-receptor matrix from NicheNetnichenet_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 datageo_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 datagse_signaling_igraph_objects.rds : list of igraph objects for 17 overlapping LRTs and their signaling mediators in the Lau et al., 2020 datasetseurat_preprocessing/geo_filtered_seurat.rds : merged and filtered seurat object of Morabito et al., 2021 datageo_integrated_seurat.rds : seurat object integrated using harmony of Morabito et al., 2021 datageo_clustered_seurat.rds : clustered seurat object of Morabito et al., 2021 datageo_processed_seurat.rds : processed seurat object with final cell type assignments at specified resolution of Morabito et al., 2021 datagse_filtered_seurat.rds : merged and filtered seurat object of Lau et al., 2020 datagse_integrated_seurat.rds : seurat object integrated using harmony of Lau et al., 2020 datagse_clustered_seurat.rds : clustered seurat object of Lau et al., 2020 datagse_processed_seurat.rds : processed seurat object with final cell type assignments at specified resolution of Lau et al., 2020 data
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