PBMC: Normal Human Peripheral Blood Mononuclear Cells (PBMCs)

In JonathanIrish/MEMv3: Marker Enrichment Modeling (MEM)

Description

This dataset contains 49651 events from a 25-marker panel CyTOF analysis of normal human PBMCs. Expression values are the raw (pre-transformation) median intensity (MI) values.

Data has been pre-gated to include only DNA-intercalator (Iridium) positive and CD45-high events. Expert biaxial gating was used to separate these events into 7 major blood cell populations: CD4+ T cells, CD8+ T cells, IgM+ B cells, IgM- B cells, dendritic cells (DCs), natural killer (NK) cells, and monocytes. Per-cell population identity is specified in the cluster channel (variable).

This dataset is meant to be used as an example with the MEM package.

See refs for experimental protocol and further details.

Usage

data("PBMC")

Format

A data frame with 49651 observations on the following 26 variables.

The following 25 surface markers were measured by CyTOF.

CD19

B cell receptor (BCR)

CD117

c-Kit; RTK expressed by stem and progenitor cells

CD11b

ITGAM, macrophage-1 antigen; complement receptor 3

CD4

T cell receptor (TCR) co-receptor; binds antigens presented by MHC II

CD8

T cell receptor (TCR) co-receptor; binds antigens presented by MHC I

CD20

B cell surface protein

CD34

surface protein expressed by hemotopoeitic stem cells and lost over course of differentiation

CD61

surface marker expressed on platelets

CD123

Interleukin-3 receptor; expressed by progenitor cells

CD45RA

CD45 isoform expressed by Naive T lymphocytes

CD45

protein tyrosine phosphatase; expressed by all mature leukocytes

CD10

membrane metallo-endopeptidase expressed by common lymphoid progenitors

CD33

Siglec-3; expressed by myeloid cells

CD11c

complement receptor; highly expressed on dendritic cells and myeloid cells

CD14

pattern recognition receptor expressed by innate lymphoid cells

CD69

involved in signaling and proliferation of activated t-lymphocytes and natural killer cells

CD15

plays role in phagocytosis and chemotaxis; expressed in multiple blood cell malignancies

CD16

low affinity Fc receptor for IgG; expressed by natural killer cells, neutrophils, and myeloid cells

CD44

cell adhesion molecule and hyaluronic acid receptor

CD38

highly expressed on germinal center B cells and plasma cells

CD25

IL-2 receptor; expressed by activated T cells

CD3

T cell receptor (TCR)

IgM

heavy chain isoform of BCR

HLADR

MHC class II receptor

CD56

NCAM; expressed by natural killer cells

cluster

1: CD4+ T cells 2: CD8+ T cells 3: Dendritic cells (DCs) 4: IgM- B cells 5: IgM+ B cells 6: Monocytes 7: Natural killer (NK) cells

Details

The dataset should be arcsinh transformed with cofactor of 15. See MEM for more details.

Source

Leelatian et al., Methods Mol Biol, 2015.

References

Diggins et al., Methods, 2016. Diggins et al., Nature Methods, 2017

Examples

data(PBMC)
## maybe str(PBMC) ; plot(PBMC) ...

JonathanIrish/MEMv3 documentation built on July 14, 2019, 10:43 p.m.