ABSTRACT: Transcription profiling of murine J1 embryonic stem cells undergoing a differentiation time course to study changes in transcription during stem cell differentiation
Project description:Transcription profiling of murine R1 embryonic stem cells differentiating into embryoid bodies over a time-course to study changes in transcription during stem cell differentiation
Project description:Transcription profiling of murine V6.5 embryonic stem cells differentiating into embryoid bodies over a time-course to study changes in transcription during stem cell differentiation
Project description:The study of embryonic stem cell mediated neuronal differentiation allows for improved understanding of the mechanisms involved in embryonic neuronal development. We investigated expression profile changes using time course cDNA microarray to identify clues for the signaling network of neuronal differentiation. Keywords: time course, embryonic stem cell
Project description:Gene expression studies of human embryonic stem cells undergoing directed differentiation to endothelial cells to identify key transcriptional changes during differentiation
Project description:An 11-point time course study on differentiating embryoid bodies from a murine J1 embryonic stem cell line. The time course includes 0 hr, 6 hr, 12 hr, 18 hr, 24 hr, 36 hr, 48 hr, 4 days, 7 days, 9 days and 14 days. Keywords: Time course
Project description:Metabolism is vital to cellular function and tissue homeostasis during human lung development. In utero, embryonic pluripotent stem cells undergo endodermal differentiation towards a lung progenitor cell fate that can be mimicked in vitro using induced human pluripotent stem cells (hiPSCs) to study genetic mutations. To identify differences between wild type and surfactant protein B (SFTPB)-deficient cell lines during endoderm specification towards lung, we used an untargeted metabolomics approach to evaluate the developmental changes in metabolites. We found that the metabolites most enriched during the differentiation from pluripotent stem cell to lung progenitor cell, regardless of cell line, were sphingomyelins and phosphatidylcholines, two important lipid classes in fetal lung development. The SFTPB mutation had no metabolic impact on early endodermal lung development. The identified metabolite signatures during lung progenitor cell differentiation may be utilized as biomarkers for normal embryonic lung development.
Project description:Pluripotent stem cells (PSC) endocrine differentiation at a large scale allows sampling of
transcriptome and proteome with phosphoproteome (proteoform) at specific time points. We describe the dynamic time course of changes in cells undergoing directed beta cell differentiation and show target proteins or previously unknown phosphorylation of critical proteins in pancreas development, NKX6.1, and Chromogranin A (CHGA). We describe fluctuations in the correlation between gene expression, its protein abundance, and phosphorylation, which follow differentiation protocol perturbations of cell fates at all stages to id entify proteoform profiles. Our computational modeling recognizes outliers on a phenomic landscape of endocrine differentiation, and we outline several new biological pathways involved. We also suggest that non correlating proteins abundances or new phosphorylation motifs of NKX6.1 and CHGA point to new signaling pathways that may play an essential role in beta cell development.
Project description:Retinoic acid RA time course experiment: H1 cells(WiCell Research Institute, WA01, Passage40) maintained in TeSR1 were treated with 1uM retinoic acid (RA) in a detailed time course:day0,day0.5,day1,day1.5,day2,day3, day4 and day5 . Total RNA was prepared by usage of the Qiagen RNA extraction kit. mRNA was purified and then labeled and hybridized to HG17 NimbleGen human expression chips to evaluate changes in gene expression during RA-induced differentiation. Keywords: Retionic acid gene expression time series human embryonic stem cells
Project description:Generation of oligodendrocytes (OLs) is a sophisticated multistep process, mechanistic underpinnings of which are not fully understood and demand further investigation. To systematically profile proteome dynamics during human embryonic stem cell (hESC) differentiation into OLs, we applied in-depth quantitative proteomics at different developmental stages and monitored changes in protein abundance using a multiplexed tandem mass tag (TMT) based proteomics approach. Findings: Our proteome data provided a comprehensive protein expression profile that highlighted specific expression clusters based on the protein abundances over the course of human OL lineage differentiation. The proteome profile of OL lineage cells revealed 378 proteins that were specifically up-regulated only in one differentiation stage. In addition, comparative pairwise analysis of differentiation stages demonstrated that abundances of 352 proteins differentially changed between consecutive differentiation time points. Our results highlighted the eminence of the planar cell polarity (PCP) signaling and autophagy (particularly macroautophagy) in the progression of OL lineage differentiation