Tal1ChimeraData: Tal1 chimera data

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

Tal1 chimera data

Description

Obtain the processed or raw counts for the Tal1 chimeric mouse embryo dataset.

Usage

Tal1ChimeraData(
  type = c("processed", "raw"),
  samples = NULL,
  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 (four) samples.
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 E8.5 Tal1 chimera experiment from Pijuan-Sala et al. (2019). The dataset contains four 10X Genomics samples:

• Sample 1: _Tal1_ knock-out cells (tomato positive)

• Sample 2: _Tal1_ knock-out cells (tomato positive)

• Sample 3: wild-type cells (tomato negative)

• Sample 4: wild-type cells (tomato negative)

All samples are from E8.5, from the same pool of chimeric embryos. Different samples with the same Tomato status are therefore technical replicates of each other.

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, number of the sample from which the cell was taken.

stage:

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

tomato:

Logical, whether this cell expressed td-Tomato during FACS.

stage.mapped:

Character, stage of the mouse embryo atlas to which the cell was mapped.

celltype.mapped:

Character, cell type of the mouse embryo atlas to which the cell was mapped.

Reduced dimension representations of the data are also available in the reducedDims slot of the SingleCellExperiment object.

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

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

tal1.data <- Tal1ChimeraData(samples = 1)

tal1.data <- Tal1ChimeraData(type="processed", samples = 1)

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