Quantitative Analysis of Transcription Dynamics in Pluripotent and Differentiated Cells

Cellular identity is a direct consequence of the transcriptional output for any given cell type. Understanding the regulatory properties of the genes that define each cell type is of fundamental importance. In this study, we performed a detailed characterization of the gene expression profiles in embryonic stem cells (ESC) and three terminally differentiated primary cell types. Using deep chromatin RNA sequencing (~500 million mapped reads), we were able to accurately quantify transcripts for genes expressed at very low levels. This provides us with the ability to distinguish genes that exhibit a broad dynamic range among cell types from those whose dynamic range of expression is more limited. Strand specific sequencing of chromatin associated transcripts in Embryonic Stem cells and three primary cell types; E14.5 Cortial Neurons, CD4+ CD8+ Thymocytes and Bone Marrow Derived Macrophages