Dataset Open Access

Single Cell RNAseq of Mouse Testis

Wells; Myers; Conrad; Jung

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

R object files, to load in R use readRDS(), or the load2() function from the associated testisAtlas package.
Files (657.8 MB)
Name Size
cell_imputation_AUCs.rds
md5:87bb482c1b934db269cdd2a4f509fcad
1.1 MB Download
HocomocoV11_motifProbs_matrix.rds
md5:4726e5e458fa69bcd46079acd54d5ef3
181.9 MB Download
motifFinder_denovo.rds
md5:9e0ba1ec52ec52793a953f0cb35064ad
82.0 MB Download
motifFinder_denovo_fixed.rds
md5:bae43b6694622c9617900e7bef87ab8a
75.8 MB Download
QC_count_matrix.rds
md5:7931bc63e1c1344e437936133c141dc9
61.5 MB Download
SDA_objects.zip
md5:d60ca9f64f40c510e77bfca628f58f62
244.8 MB Download
tomtom_matched_motifs.rds
md5:35459672048fa04bb8993ba17831ae3d
10.6 MB Download
  • https://doi.org/10.1101/393769

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