NovershternHematopoieticData: Obtain bulk microarray expression for sorted hematopoietic...

In LTLA/celldex: Index of Reference Cell Type Datasets

Obtain bulk microarray expression for sorted hematopoietic cells

Description

Download and cache the normalized expression values of 211 bulk human microarray samples of sorted hematopoietic cell populations that can be found in GSE24759.

Usage

NovershternHematopoieticData(
  ensembl = FALSE,
  cell.ont = c("all", "nonna", "none"),
  legacy = FALSE
)

Arguments

ensembl	Logical scalar indicating whether to convert row names to Ensembl IDs. Genes without a mapping to a non-duplicated Ensembl ID are discarded.
cell.ont	String specifying whether Cell Ontology terms should be included in the colData. If "nonna", all samples without a valid term are discarded; if "all", all samples are returned with (possibly NA) terms; if "none", terms are not added.
legacy	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

Details

The dataset contains 211 human microarray samples annotated to 16 main cell types ("label.main"):

• Basophils

• B cells

• CMPs

• Dendritic cells

• Eosinophils

• Erythroid cells

• GMPS

• Granulocytes

• HSCs

• Megakaryocytes

• MEPs

• Monocytes

• NK cells

• NK T cells

• CD8+ T cells

• CD4+ T cells

Samples were additionally annotated to 38 fine cell types ("label.fine"):

• Basophils

• Naive B cells

• Mature B cells class able to switch

• Mature B cells

• Mature B cells class switched

• Common myeloid progenitors

• Plasmacytoid Dendritic Cells

• Myeloid Dendritic Cells

• Eosinophils

• Erythroid_CD34+ CD71+ GlyA-

• Erythroid_CD34- CD71+ GlyA-

• Erythroid_CD34- CD71+ GlyA+

• Erythroid_CD34- CD71lo GlyA+

• Erythroid_CD34- CD71- GlyA+

• Granulocyte/monocyte progenitors

• Colony Forming Unit-Granulocytes

• Granulocyte (Neutrophilic Metamyelocytes)

• Granulocyte (Neutrophils)

• Hematopoietic stem cells_CD133+ CD34dim

• Hematopoietic stem cell_CD38- CD34+

• Colony Forming Unit-Megakaryocytic

• Megakaryocytes

• Megakaryocyte/erythroid progenitors

• Colony Forming Unit-Monocytes

• Monocytes

• Mature NK cells_CD56- CD16+ CD3-

• Mature NK cells_CD56+ CD16+ CD3-

• Mature NK cells_CD56- CD16- CD3-

• NK T cells

• Early B cells

• Pro B cells

• CD8+ Effector Memory RA

• Naive CD8+ T cells

• CD8+ Effector Memory

• CD8+ Central Memory

• Naive CD4+ T cells

• CD4+ Effector Memory

• CD4+ Central Memory

The subtypes have also been mapped to the Cell Ontology ("label.ont", if cell.ont is not "none"), which can be used for further programmatic queries.

Value

A SummarizedExperiment object with a "logcounts" assay containing the log-normalized expression values, along with cell type labels in the colData.

Author(s)

Jared Andrews

References

Novershtern N et al. (2011). Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144, 296-309.

Examples

ref.se <- NovershternHematopoieticData()

LTLA/celldex documentation built on June 3, 2024, 4:53 p.m.