MouseDropletData: Mouse ageing thymus droplet single-cell RNA-sequencing data

In MarioniLab/MouseThymusAgeing: Single-cell Transcriptomics Data of the Ageing Mouse Thymus

Mouse ageing thymus droplet single-cell RNA-sequencing data

Description

Obtain the processed counts for the mouse ageing thymus droplet scRNA-seq data set.

Usage

MouseDropletData(samples = NULL)

Arguments

samples

Integer or character vector specifying the samples for which data should be obtained. If NULL (default), data are returned for all (6) samples.

Details

This function downloads the data for the mouse ageing thymus droplet scRNA-seq data from Baran-Gale et al. (2020).

The dataset contains 6 10X Genomics samples. The available samples are: ZsG_1stRun1, ZsG_1stRun2, ZsG_2ndRun1, ZsG_2ndRun2, ZsG_3rdRun1, ZsG_3rdRun2.

In the data, cell-containing libraries have already been identified in each sample using the emptyDrops function from DropletUtils. The count matrix contains the raw count vectors for the cells called from all samples in this manner. Size factors were computed using the computeSumFactors function from scran. The column metadata for called cells contains:

CellID:

Character, unique cell identifier across all samples.

SampID:

Character, Short unique identified for the experimental sample.

Class:

Character, Either Singlet or Multiplet Identifies cells called as a multiplet from hash-tag demultiplexing.

HTO:

Character, Hashtag oligo (HTO) character identifier, used for multiplexing experimental samples.

Age:

Character, Age of mouse at the time of doxycycline treatment. Age at time of data acquisition is +4weeks.

SortType:

Character, Flow cytometry sorting group, either ZsGreen+ (ZsGp) or ZsGreen- (ZsGn).

Cluster:

Integer, Cluster to which cells were assigned based on using the Walktrap community detection algorithm on a k-NN graph.

ClusterAnnot:

Character, Annotation assigned to cluster.

SizeFactor:

Numeric, Estimated normalized factor across all cells and experimental samples.

Reduced dimension representations of the data are also available in the reducedDims slot of the SingleCellExperiment object. The SingleCellExperiment object has row metadata that contains the Ensembl ID ensembl_gene_id and Gene symbols external_gene_name for each gene, as well as gene chromosome, strand and both start and end positions.

Value

A SingleCellExperiment is returned containing processed data from selected samples.

List elements are named after the corresponding sample.

Author(s)

Mike Morgan, based on original code by Aaron Lun & Jonathan Griffiths

Mike Morgan

References

Baran-Gale J, Morgan MD, et al. (2020) Ageing compromises mouse thymus function and remodels epithelial cell differentiation eLife 9:e56221.

Examples

drop.data <- MouseDropletData(samples = "ZsG_1stRun1")
drop.data

MarioniLab/MouseThymusAgeing documentation built on Feb. 19, 2023, 11:24 a.m.