MouseSMARTseqData: Mouse ageing thymus SMART-seq2 single-cell RNA-sequencing...

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

Mouse ageing thymus SMART-seq2 single-cell RNA-sequencing data

Description

Obtain the processed counts for the mouse ageing thymus SMART-seq2 scRNA-seq data set.

Usage

MouseSMARTseqData(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 (5) 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 5 different SMART-seq2 samples, split by the day of acquisition. The available samples are: day1, day2, day3, day4, day5.

In the data, poor-quality cells have already been removed based on insufficient sequencing depth, high mitochondrial content, excessive proportion of expression from ERCC spike-in and ribosomal genes. Exact details can be found in the methods section of Baran-Gale et al. (2020).

The count matrix contains the raw count vectors for the cells that pass QC. 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.

ClusterID:

Numeric, The cluster to which cells were assigned based on community detection on a shared-NN grpah.

Position:

Character, Plate position of the index-sorted cell (384 well plate format).

PlateID:

Character, A unique ID for the 384-well plate into which each cell was index-sorted.

Column:

Integer, A value from 1-24 corresponding to the plate column.

Row:

Character, A value from A-P corresponding to the plate row.

SortType:

Character, Flow cytometry sorting group, mTEClo, mTEChi, gmTEC or cTEC.

SortDay:

Integer, Day on which cells were sorted - corresponds to the sample IDs for downloading data and replicate.

Age:

Character, Mouse age at the time of data acquisition.

SubType:

Character, Annotation assigned to clusters.

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

smart.data <- MouseSMARTseqData(samples = "day1")
smart.data

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