Single Cell RNAseq of Mouse Testis

This is the processed data from the publication: "Unified single-cell analysis of testis gene regulation and pathology in 5 mouse strains" (https://doi.org/10.1101/393769)

The raw data is avaliable at GEO: GSE113293

Associated software is at https://zenodo.org/badge/latestdoi/140632831

SDA_objects.zip contains key tables required for many functions, download this to use the shiny app. Contents:

• cell_data: data.table containing metadata of the cells. 80 columns including cell id, SDA component cell scores, Tsne coordinates, pseudotime, experimental group etc.
• data: a sparse matrix of normalised read counts (20322 cells by 19262 genes)
• gene_annotations: data.table containing gene locations, enrichment vs other tissues from bulk data, infertility gene status
• GO_enrich: data.table containing gene ontology enrichments for each component, the genes enriched, p.values and enrichment values
• principal_curves: list of output of princurve() containing the pseudotime trajetories
• SDAresults: output of SDA run loaded using SDAtools::load_results()

Other R objects include:

• QC_count_matrix: Sparse matrix of raw count values for QC cells and genes
• cell_imputation_AUCs: data.table of PRAC AUC values for unimputed (train), mean cell, SDA (predict), ICA, PCA, NNMF, and MAGIC
• HocomocoV11_motifProbs_matrix: Matrix of regulation probabilities from MotifFinder using fixed motifs from HocomocoV11 database
• motifFinder_denovo: list of results of MotifFinder denovo motifs from promoters regions of genes from each component
• motifFinder_denovo_fixed: list of results of MotifFinder using 125 denovo motifs with fixed motif on all genes.
• tomtom_matched_motifs: data.table of TOMTOM matches of denovo motifs, plus metadata