TChimeraData: T chimera data

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

T chimera data

Description

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

Usage

TChimeraData(
  type = c("processed", "raw"),
  samples = c(1:2, 5:16),
  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 QC-passing (fourteen) 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 T chimera experiment from Guibentif et al. (2020). The dataset contains sixteen 10X Genomics samples from sets of embryo pools:

• Sample 1: E8.5 injected cells (tomato positive), pool 1

• Sample 2: E8.5 host cells (tomato negative), pool 1

• Sample 3: E7.5 injected cells (tomato positive), pool 2

• Sample 4: E7.5 host cells (tomato negative), pool 2

• Sample 5: E8.5 injected cells (tomato positive), pool 3

• Sample 6: E8.5 host cells (tomato negative), pool 3

• Sample 7: E8.5 injected cells (tomato positive), pool 4

• Sample 8: E8.5 host cells (tomato negative), pool 4

• Sample 9: E8.5 injected cells (tomato positive), pool 5

• Sample 10: E8.5 host cells (tomato negative), pool 5

• Sample 11: E7.5 injected cells (tomato positive), pool 6

• Sample 12: E7.5 host cells (tomato negative), pool 6

• Sample 13: E7.5 injected cells (tomato positive), pool 7

• Sample 14: E7.5 host cells (tomato negative), pool 7

• Sample 15: E7.5 injected cells (tomato positive), pool 8

• Sample 16: E7.5 host cells (tomato negative), pool 8

Samples from the same pool are paired in the experimental design. Each pool is a biological replicate. Samples 3 and 4 were excluded from analyses, as in these chimeras host cells seemed to form only ExE ectoderm. The data is available to download if you like, but will not be fetched by default.

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.

pool:

Integer, embryo pool from which cell derived; samples with same value are matched.

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.

closest.cell:

Character, closest cell in the atlas dataset (see EmbryoAtlasData) after MNN mapping.

doub.density:

Numeric, output of (a now-outdated run of) scran::doubletCells, performed on each sample separately.

trajectory.mapped:

Character, trajectory membership for somite/NMP formation.

somite.subct.mapped:

Character, somite subcluster to which cells mapped.

sizeFactor:

Numeric, cell sizefactor.

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, with modification by Jonathan Griffiths

References

Guibentif C, Griffiths JA et al. (2020). Diverse Routes towards Early Somites in the Mouse Embryo Developmental Cell In press.

Examples

t.data <- TChimeraData(samples = 1)

t.data <- TChimeraData(type="processed", samples = 1)

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