SUMMARY During embryonic development, cells must establish fates, morphologies and behaviors in coordination with one another to form a functional body. A prevalent hypothesis for how this coordination is achieved is that each cell’s fate and behavior is determined by a defined mixture of RNAs. Only recently has it become possible to measure the full suite of transcripts in a single cell. Here we quantify genome-wide mRNA abundance in each cell of the C. elegans embryo up to the 16-cell stage. We describe spatially dynamic expression, quantify cell-specific differential activation of the zygotic genome, and identify genes that were previously unappreciated as being critical for development. We present an interactive data visualization tool that allows broad access to our dataset. This genome-wide single-cell map of mRNA abundance, alongside the well-studied life history and fate of each cell, describes at a cellular resolution the mRNA landscape that guides development.

HIGHLIGHTS-RNA-seq on each cell of the early C. elegans embryo complements the known lineage -We measured the zygotic activation specific to each unique cell of the embryo -We identified genes that are functionally redundant and critical for development -We created an interactive online data visualization tool for exploring the data eTOC BLURBC. elegans is a powerful model for development, with an invariant and completely described cell lineage. To enrich this resource, we performed single-cell RNA-seq on each cell of the embryo through the 16-cell stage. Zygotic genome activation is differential between cell types. We identified hundreds of candidates for partially redundant genes, and verified one such set as critical for development. We created an interactive online data visualization tool to invite others to explore our dataset. SUMMARYDuring embryonic development, cells must establish fates, morphologies and behaviors in coordination with one another to form a functional body. A prevalent hypothesis for how this coordination is achieved is that each cell's fate and behavior is determined by a defined mixture of RNAs. Only recently has it become possible to measure the full suite of transcripts in a single cell. Here we quantify the abundance of every mRNA transcript in each cell of the C. elegans . CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/047746 doi: bioRxiv preprint first posted online Apr. 8, 2016; 2 embryo up to the 16-cell stage. We describe spatially dynamic expression, quantify cell-specific differential activation of the zygotic genome, and identify critical developmental genes previously unappreciated because of their partial redundancy. We present an interactive data visualization tool that allows broad access to our dataset. This genome-wide single-cell map of mRNA abundance, alongside the well-studied life history and fates of each cell, describes at a cellular resolution the mRNA landscape that guides development.

The information expressed in humanities datasets is inextricably tied to a wider discursive environment that is irreducible to complete formal representation. Humanities scholars must wrestle with this fact when they attempt to publish or consume structured data. The practice of "nanopublication," which originated in the e-science domain, offers a way to maintain the connection between formal representations of humanities data and its discursive basis. In this paper we describe nanopublication, its potential applicability to the humanities, and our experience curating humanities nanopublications in the PeriodO period gazetteer.

The PeriodO project seeks to fill a gap in the landscape of digital antiquity through the creation of a Linked Data gazetteer of period definitions that transparently record the spatial and temporal boundaries assigned to a given period by an authoritative source. Our presentation of the PeriodO gazetteer is prefaced by a history of the role of periodization in the study of the past, and an analysis of the difficulties created by the use of periods for both digital data visualization and integration. This is followed by an overview of the PeriodO data model, a description of the platform's architecture, and a discussion of the future direction of the project.

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Summary Differential Expression Gene Explorer (DrEdGE) is a web-based tool that guides genomicists through easily creating interactive online data visualizations, which colleagues can query according to their own conditions to discover genes, samples or patterns of interest. We demonstrate DrEdGE’s features with three example websites generated from publicly available datasets—human neuronal tissue, mouse embryonic tissue and Caenorhabditis elegans whole embryos. DrEdGE increases the utility of large genomics datasets by removing technical obstacles to independent exploration. Availability and implementation Freely available at http://dredge.bio.unc.edu. Supplementary information Supplementary data are available at Bioinformatics online.

The PeriodO period gazetteer collects definitions of time periods made by archaeologists and other historical scholars. In constructing the gazetteer, we sought to make period definitions parsable and comparable by computers while also retaining the broader scholarly context in which they were conceived. Our approach resulted in a dataset of period definitions and their provenances that resemble what data scientists working in the e-science domain have dubbed "nanopublications." In this paper we describe the origin and goals of nanopublications, provide an overview of the design and implementation of a database of period definitions, and highlight the similarities and differences between the two.

Abstract:We