mulvey2015: Data from Mulvey et al. 2015

In lgatto/pRolocdata: Data accompanying the pRoloc package

Data from Mulvey et al. 2015

Description

This is the data from Mulvey et al., Dynamic proteomic profiling of extra-embryonic endoderm differentiation in mouse embryonic stem cells. , Stem Cell. (PMID 26059426). See below for more details.

Usage

data(mulvey2015)
data(mulvey2015norm)

Format

The data are instances of class MSnSet from package MSnbase. This ending with _se are of class SummarizedExperiment.

Details

While not a spatial proteomics data, it was analysed with the pRoloc package.

During mammalian preimplantation development, the cells of the blastocyst's inner cell mass differentiate into the epiblast and primitive endoderm lineages, which give rise to the fetus and extra-embryonic tissues, respectively. Extra-embryonic endoderm (XEN) differentiation can be modeled in vitro by induced expression of GATA transcription factors in mouse embryonic stem cells. Here, we use this GATA-inducible system to quantitatively monitor the dynamics of global proteomic changes during the early stages of this differentiation event and also investigate the fully differentiated phenotype, as represented by embryo-derived XEN cells. Using mass spectrometry-based quantitative proteomic profiling with multivariate data analysis tools, we reproducibly quantified 2,336 proteins across three biological replicates and have identified clusters of proteins characterized by distinct, dynamic temporal abundance profiles. We first used this approach to highlight novel marker candidates of the pluripotent state and XEN differentiation. Through functional annotation enrichment analysis, we have shown that the downregulation of chromatin-modifying enzymes, the reorganization of membrane trafficking machinery, and the breakdown of cell-cell adhesion are successive steps of the extra-embryonic differentiation process. Thus, applying a range of sophisticated clustering approaches to a time-resolved proteomic dataset has allowed the elucidation of complex biological processes which characterize stem cell differentiation and could establish a general paradigm for the investigation of these processes.

References

Mulvey CM, Schr\"oter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS. Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells. Stem Cells. 2015 Sep;33(9):2712-25. doi: 10.1002/stem.2067. Epub 2015 Jun 23. PubMed PMID: 26059426.

Examples

data(mulvey2015)
library("pRoloc")
plot2D(mulvey2015)

data(mulvey2015norm)
heatmap(exprs(mulvey2015))

library(SummarizedExperiment)
data(mulvey2015_se)
mulvey2015_se

lgatto/pRolocdata documentation built on Oct. 17, 2024, 10:16 p.m.