EmbryoAtlasData: Mouse gastrulation timecourse data

In MarioniLab/MouseGastrulationData: Single-Cell -omics Data across Mouse Gastrulation and Early Organogenesis

Mouse gastrulation timecourse data

Description

Obtain the processed or raw counts for the mouse gastrulation scRNAseq dataset.

Usage

EmbryoAtlasData(
  type = c("processed", "raw"),
  samples = NULL,
  get.spliced = FALSE,
  Csparse.assays = TRUE
)

Arguments

type	String specifying the type of data to obtain, see Details. Default behaviour is to return processed data.
samples	Integer or character vector specifying the samples for which data (processed or raw) should be obtained. If NULL (default), data are returned for all (36) samples.
get.spliced	Logical indicating whether to also download the spliced/unspliced/ambiguously spliced count matrices.
Csparse.assays	Logical indicating whether to convert assay matrices into the column major format that is more performant with contemporary software packages. Default behaviour is to perform the conversion.

Details

This function downloads the data for the embryo atlas from Pijuan-Sala et al. (2019). The dataset contains 36 10X Genomics samples; sample 11 is absent due to QC failure. The AtlasSampleMetadata variable contains information about each of these samples.

In the processed 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:

cell:

Character, unique cell identifier across all samples.

barcode:

Character, cell barcode from the 10X Genomics experiment.

sample:

Integer, index of the sample from which the cell was taken.

pool:

Integer, index of the embryo pool from which the sample derived. Samples with the same value are technical, not biological, replicates

stage:

Character, stage of the mouse embryo at which the sample was taken.

sequencing.batch:

Integer, sequencing run in which sample was multiplexed.

theiler:

Character, Theiler stage from which the sample was taken; alternative scheme to stage.

doub.density:

Numeric, output of (a now-outdated run of) scran::doubletCells, performed on each sample separately.

doublet:

Logical, whether a cell was called as a doublet.

cluster:

Integer, top-level cluster to which cell was assigned across all samples.

cluster.sub:

Integer, cluster to which cell was assigned when clustered within each cluster.

cluster.stage:

Integer, top-level cluster to which cell was assigned within individual timepoints.

cluster.theiler:

Integer, top-level cluster to which cell was assigned within individual Theiler stages.

stripped:

Logical, whether a cell was called as a cytoplasm-stripped nucleus.

celltype:

Character, cell type to which the cell was assigned.

colour:

Integer, cell type colour (hex) as in Pijuan-Sala et al. (2019).

Reduced dimension representations of the data are also available in the reducedDims slot of the SingleCellExperiment object. These are pca.corrected and umap.

If spliced counts were requested, these will be in the assays slot of the SingleCellExperiment object. Spliced count matrices were collated using velocyto version 0.17.17. Spliced count matrices will not have had swapped molecules removed, as velocyto and DropletUtils::swappedDrops are not compatible. However, these should still be effective for calculating RNA velocity estimates using various different tools.

The raw data contains the unfiltered count matrix for each sample, as generated directly from the CellRanger software. Swapped molecules have been removed using DropletUtils::swappedDrops. No filtering has been performed to identify cells. This may be useful if performing analyses that need to account for the ambient RNA pool.

For both raw and processed data, the row metadata contains the Ensembl ID and MGI symbol for each gene.

Value

If type="processed", a SingleCellExperiment is returned containing processed data from selected samples.

If type="raw", a List of SingleCellExperiments is returned, each containing the raw counts for a single sample. List elements are named after the corresponding sample.

Author(s)

Aaron Lun, with modification by Jonathan Griffiths

References

Pijuan-Sala B, Griffiths JA, Guibentif C et al. (2019). A single-cell molecular map of mouse gastrulation and early organogenesis. Nature 566, 7745:490-495.

Examples

atlas.data <- EmbryoAtlasData(samples = 1:2)

atlas.data <- EmbryoAtlasData(type="processed", samples = 1:2)

MarioniLab/MouseGastrulationData documentation built on Jan. 31, 2024, 11:01 a.m.