BackgroundHuman pluripotent stem cells offer the best available model to study the underlying cellular and molecular mechanisms of human embryonic lineage specification. However, it is not fully understood how individual stem cells exit the pluripotent state and transition towards their respective progenitor states.ResultsHere, we analyze the transcriptomes of human embryonic stem cell-derived lineage-specific progenitors by single-cell RNA-sequencing (scRNA-seq). We identify a definitive endoderm (DE) transcriptomic signature that leads us to pinpoint a critical time window when DE differentiation is enhanced by hypoxia. The molecular mechanisms governing the emergence of DE are further examined by time course scRNA-seq experiments, employing two new statistical tools to identify stage-specific genes over time (SCPattern) and to reconstruct the differentiation trajectory from the pluripotent state through mesendoderm to DE (Wave-Crest). Importantly, presumptive DE cells can be detected during the transitory phase from Brachyury (T)+ mesendoderm toward a CXCR4+ DE state. Novel regulators are identified within this time window and are functionally validated on a screening platform with a T-2A-EGFP knock-in reporter engineered by CRISPR/Cas9. Through loss-of-function and gain-of-function experiments, we demonstrate that KLF8 plays a pivotal role modulating mesendoderm to DE differentiation.ConclusionsWe report the analysis of 1776 cells by scRNA-seq covering distinct human embryonic stem cell-derived progenitor states. By reconstructing a differentiation trajectory at single-cell resolution, novel regulators of the mesendoderm transition to DE are elucidated and validated. Our strategy of combining single-cell analysis and genetic approaches can be applied to uncover novel regulators governing cell fate decisions in a variety of systems.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1033-x) contains supplementary material, which is available to authorized users.

We demonstrate high-performance, flexible, transparent heaters based on large-scale graphene films synthesized by chemical vapor deposition on Cu foils. After multiple transfers and chemical doping processes, the graphene films show sheet resistance as low as ∼43 Ohm/sq with ∼89% optical transmittance, which are ideal as low-voltage transparent heaters. Time-dependent temperature profiles and heat distribution analyses show that the performance of graphene-based heaters is superior to that of conventional transparent heaters based on indium tin oxide. In addition, we confirmed that mechanical strain as high as ∼4% did not substantially affect heater performance. Therefore, graphene-based, flexible, transparent heaters are expected to find uses in a broad range of applications, including automobile defogging/deicing systems and heatable smart windows.

Oscillatory gene expression is fundamental to mammalian development, but technologies to monitor expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applications to a number of data sets demonstrate the utility of the approach and also identify a potential artifact in the Fluidigm C1 platform.

Preventing reactive gas species such as oxygen or water is important to ensure the stability and durability of organic electronics. Although inorganic materials have been predominantly employed as the protective layers, their poor mechanical property has hindered the practical application to flexible electronics. The densely packed hexagonal lattice of carbon atoms in graphene does not allow the transmission of small gas molecules. In addition, its outstanding mechanical flexibility and optical transmittance are expected to be useful to overcome the current mechanical limit of the inorganic materials. In this paper, we reported the measurement of the water vapor transmission rate (WVTR) through the 6-layer 10 × 10 cm(2) large-area graphene films synthesized by chemical vapor deposition (CVD). The WVTR was measured to be as low as 10(-4) g/m(2)·day initially, and stabilized at ∼0.48 g/m(2)·day, which corresponds to 7 times reduction in WVTR compared to bare polymer substrates. We also showed that the graphene-passivated organic field-effect transistors (OFETs) exhibited excellent environmental stability as well as a prolonged lifetime even after 500 bending cycles with strain of 2.3%. We expect that our results would be a good reference showing the graphene's potential as gas barriers for organic electronics.

Astrocytes display diverse morphologies in different regions of the central nervous system. Whether astrocyte diversity is attributable to developmental processes and bears functional consequences, especially in humans, is unknown. RNA-seq of human pluripotent stem cell-derived regional astrocytes revealed distinct transcript profiles, suggesting differential functional properties. This was confirmed by differential calcium signaling as well as effects on neurite growth and blood-brain barrier formation. Distinct transcriptional profiles and functional properties of human astrocytes generated from regionally specified neural progenitors under the same conditions strongly implicate the developmental impact on astrocyte diversity. These findings provide a rationale for renewed examination of regional astrocytes and their role in the pathogenesis of psychiatric and neurological disorders.