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Single-cell RNA-Sequencing (scRNA-Seq) has undergone major technological advances in recent years, enabling the conception of various organism-level cell atlassing projects. With increasing numbers of datasets being deposited in public archives, there is a need to address the challenges of enabling the reproducibility of such data sets. Here, we describe guidelines for a minimum set of metadata to sufficiently describe scRNA-Seq experiments, ensuring reproducibility of data analyses.

The amount of public proteomics data is increasing at an extraordinary rate. Hundreds of datasets are submitted each month to ProteomeXchange repositories, representing many types of proteomics studies, focusing on different aspects such as quantitative experiments, post-translational modifications, protein-protein interactions, or subcellular localization, among many others. For every proteomics dataset, two levels of data are captured: the dataset description, and the data files (encoded in different file formats). Whereas the dataset description and data file formats are supported by all ProteomeXchange partner repositories, there is no standardized format to properly describe the sample metadata and their relationship with the dataset files in a way that fully allows their understanding or re-analysis. It is left to the user’s choice whether to provide or not an ad hoc document containing this information. Therefore, in many cases, understanding the study design and data requires going back to the associated publication. This can be tedious and may be restricted in the case of non-open access publications. In many cases, this problem limits the generalization and reuse of public proteomics data.Here we present a standard representation for sample metadata tailored to proteomics datasets produced by the HUPO Proteomics Standards Initiative and supported by ProteomeXchange resources. We repurposed the existing data format MAGE-TAB used routinely in the transcriptomics field to represent and annotate proteomics datasets. MAGETAB-Proteomics defines a set of annotation rules that the datasets submitted to ProteomeXchange should follow, ranging from sample properties to data analysis protocols. We also introduce a crowdsourcing project that enabled the manual curation of over 200 public datasets using MAGE-TAB-Proteomics. In addition, we describe an ecosystem of tools and libraries that were developed to validate and submit sample metadata-related information to ProteomeXchange. We expect that these tools will improve the reproducibility of published results and facilitate the reanalysis and integration of public proteomics datasets.

The outcome of the Notch pathway on proliferation depends on cellular context, being growth promotion in some, including several cancers, and growth inhibition in others. Such disparate outcomes are evident in Drosophila wing discs, where Notch overactivation causes hyperplasia despite having localized inhibitory effects on proliferation. To understand the underlying mechanisms, we have used genomic strategies to identify the Notch-CSL target genes directly activated during wing disc hyperplasia. Among them were genes involved in both autonomous and non-autonomous regulation of proliferation, growth and cell death, providing molecular explanations for many characteristics of Notch induced wing disc hyperplasia previously reported. The Notch targets exhibit different response patterns, which are shaped by both positive and negative feed-forward regulation between the Notch targets themselves. We propose, therefore, that both the characteristics of the direct Notch targets and their cross-regulatory relationships are important in coordinating the pattern of hyperplasia., This genome-wide approach characterizes the repertoire of Notch targets in proliferative growth. Extensive functional categorizations offer significant new insights into regulatory circuits that govern Notch-mediated hyperplasia.

Females of the Indian meal moth, Plodia interpunctella, and females of the Mediterranean flour month, Ephestia kuehniella (both Lepidoptera: Pyralidae), exhibit daily rhythms in calling behavior. The peak in P. interpunctella calling occurs at dusk, whereas E. kuehniella calls preferentially at dawn. This behavior turned arrhythmic in P. interpunctella females in constant darkness (DD) and remained arrhythmic in constant light (LL), whereas E. kuehniella females showed a persistent rhythm in DD and suppression of the behavior in LL, indicating regulation by a circadian clock mechanism. The rhythm of male locomotor activity corresponded well with the sexual activity of females, reaching the peak at dusk in P. interpunctella and at dawn in E. kuehniella. An immunohistochemical study of the pheromone biosynthesis activating neuropeptide, corazonin, and pigment dispersing factor revealed distinct sets of neurons in the brain-subesophageal complex and in the neurohemal organs of the 2 species.

Juvenile hormone (JH), a sesquiterpenoid produced by the insect corpus allatum gland (CA), prevents metamorphosis in larvae and stimulates vitellogenesis in adult females. Whether the same JH signaling pathway regulates both processes is presently unknown. Here, we employ the robust JH response during reproduction and development of the linden bug, Pyrrhocoris apterus, to compare the function of key JH-signaling genes encoding the JH receptor, Methoprene-tolerant (Met), its binding partner Taiman (Tai), and a JH-inducible protein, Kruppel-homolog 1 (Kr-h1). RNA interference (RNAi) with Met or Tai, but not Kr-h1, blocked ovarian development and suppressed vitellogenin gene expression in the fat body of females raised under reproduction-inducing conditions. Loss of Met and Tai matched the effects of CA ablation or the natural absence of JH during reproductive diapause. Stimulation of vitellogenesis by treatment of diapausing females with a JH mimic methoprene also required both Met and Tai in the fat body, whereas Kr-h1 RNAi had no effect. Therefore, the Met-Tai complex likely functions as a JH receptor during vitellogenesis. In contrast to Met and Kr-h1 that are both required for JH to prevent precocious metamorphosis in P. apterus larvae, removal of Tai disrupted larval ecdysis without causing premature adult development. Our results show that while Met operates during metamorphosis in larvae and reproduction in adult females, its partner Tai is only required for the latter. The diverse functions of JH thus likely rely on a common receptor whose actions are modulated by distinct components.