Published August 7, 2018
| Version 1.1.0
Dataset
Open
Single Cell RNAseq of Mouse Testis
Description
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
Notes
Files
SDA_objects.zip
Files
(657.8 MB)
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Additional details
Related works
- Is supplement to
- 10.5281/zenodo.1311482 (DOI)