Deep sequencing of transcript levels in pluripotent stem cells and their differentiated derivatives in all three germ layers

Human pluripotent stem cells (hESCs) are an excellent model to dissect the transcriptional changes that direct cell fate decisions and lineage specification during development. Utilizing directed differentiation protocols to derive definitive endoderm, splanchnic mesoderm, neural progenitor cells (NPCs), and pre-neural crest stem cells (NCSCs) from hESCs. Transcriptional profiling via RNA-seq on hESCs and cells differentiated to all three germ layers revealed lineage specific transcriptional networks that remodeled many cell processes, including epigenetic status, cell surface markers, cell cycle profiles, metabolic flux, and cellular signaling pathways. From this data we were able to verify that metabolic flux within NPCs and pre-NCSCs are regulated in a lineage specific manner that is distinct from endoderm and mesoderm formation. Overall design: Profiles of mRNA transcripts levels were generated for 5 cell types by deep sequencing, in duplicate, on a Illumina Hisec 2500 platform. Cell types analyzed were WA09 human embryonic stem cells (hESCs), as the control sample, and 4 WA09 hESC-derived cell types: definitive endoderm (DE), splanchnic mesoderm (MESO), neural progenitor cells (NPCs) and pre-neural crest cells (NCSCs).