Project description:Transcriptional profiling of a directed differentiation time course converting human embryonic stem cells (hES) into immature pancreatic beta cell precursors.
Project description:miRNA transcript profiling of a directed differentiation time course converting human embryonic stem cells (hES) into immature pancreatic beta cell precursors.
Project description:H3K4me3 ChIP-Seq profiling of a directed differentiation time course converting human embryonic stem cells (hES) into immature pancreatic beta cell precursors. CyT49, a Viacyte proprietary male hESC line with normal karyotype was used.
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:We interrogated the genome-wide occupancy of histone modifications and RNA polymerase II at several stages of an mouse embryonic stem cell to cardiomyocyte directed differentiation protocol. These four stages represent timepoints when differentiating cultures are enriched for embryonic stem cells (ESC), mesodermal cells (MES), cardiac precursors (CP), or cardiomyocytes (CM) respectively. This study revealed many dynamic patterns of histone modifications during differentiation that are coordinated with stage-specific gene expression including a novel preactivation chromatin pattern found at genes associated with cardiac function. In addition, this study identified distal enhancer elements and enriched transcription factor motifs within enhancer regions for each stage of differentiation, which were used to predict novel transcription regulatory networks. ChIP-seq analysis of histone modifications and RNA polymerase II at 4 stages of directed cardiac differentiation of mouse embryonic stem cells. Each stage in biological duplicate or triplicate
