Abstract
The more than 1000 single-cell transcriptomics studies that have been published to date constitute a valuable and vast resource for biological discovery. While various ‘atlas’ projects have ...collated some of the associated datasets, most questions related to specific tissue types, species or other attributes of studies require identifying papers through manual and challenging literature search. To facilitate discovery with published single-cell transcriptomics data, we have assembled a near exhaustive, manually curated database of single-cell transcriptomics studies with key information: descriptions of the type of data and technologies used, along with descriptors of the biological systems studied. Additionally, the database contains summarized information about analysis in the papers, allowing for analysis of trends in the field. As an example, we show that the number of cell types identified in scRNA-seq studies is proportional to the number of cells analysed.
Database URL: www.nxn.se/single-cell-studies/gui
Abstract
WormBase (www.wormbase.org) is the central repository for the genetics and genomics of the nematode Caenorhabditis elegans. We provide the research community with data and tools to ...facilitate the use of C. elegans and related nematodes as model organisms for studying human health, development, and many aspects of fundamental biology. Throughout our 22-year history, we have continued to evolve to reflect progress and innovation in the science and technologies involved in the study of C. elegans. We strive to incorporate new data types and richer data sets, and to provide integrated displays and services that avail the knowledge generated by the published nematode genetics literature. Here, we provide a broad overview of the current state of WormBase in terms of data type, curation workflows, analysis, and tools, including exciting new advances for analysis of single-cell data, text mining and visualization, and the new community collaboration forum. Concurrently, we continue the integration and harmonization of infrastructure, processes, and tools with the Alliance of Genome Resources, of which WormBase is a founding member.
The poseidon syringe pump and microscope system is an open source alternative to commercial systems. It costs less than $400 and can be assembled in under an hour using the instructions and source ...files available at https://pachterlab.github.io/poseidon . We describe the poseidon system and use it to illustrate design principles that can facilitate the adoption and development of open source bioinstruments. The principles are functionality, robustness, safety, simplicity, modularity, benchmarking, and documentation.
We describe a workflow for preprocessing of single-cell RNA-sequencing data that balances efficiency and accuracy. Our workflow is based on the kallisto and bustools programs, and is near optimal in ...speed with a constant memory requirement providing scalability for arbitrarily large datasets. The workflow is modular, and we demonstrate its flexibility by showing how it can be used for RNA velocity analyses.
Conditioned taste aversion (CTA) is a form of one-trial learning dependent on basolateral amygdala projection neurons (BLApn). Its underlying cellular and molecular mechanisms remain poorly ...understood. RNAseq from BLApn identified changes in multiple candidate learning-related transcripts including the expected immediate early gene
and
, a master kinase of the AMP-related kinase pathway with important roles in growth, metabolism and development, but not previously implicated in learning. Deletion of
in BLApn blocked memory prior to training, but not following it and increased neuronal excitability. Conversely, BLApn had reduced excitability following CTA. BLApn knockout of a second learning-related gene,
, also increased excitability and impaired learning. Independently increasing BLApn excitability chemogenetically during CTA also impaired memory. STK11 and C-FOS activation were independent of one another. These data suggest key roles for
and
in CTA long-term memory formation, dependent at least partly through convergent action on BLApn intrinsic excitability.
Single-cell transcriptomic platforms provide an opportunity to map an organism’s response to environmental cues with high resolution. Here, we applied single-nucleus RNA sequencing (snRNA-seq) to ...establish the tissue and cell type-resolved transcriptome of the adult C. elegans and characterize the inter- and trans-generational transcriptional impact of ethanol. We profiled the transcriptome of 41,749 nuclei resolving into 31 clusters, representing a diverse array of adult cell types including syncytial tissues. Following exposure to human-relevant doses of alcohol, several germline, striated muscle, and neuronal clusters were identified as being the most transcriptionally impacted at the F1 and F3 generations. The effect on germline clusters was confirmed by phenotypic enrichment analysis as well as by functional validation, which revealed a remarkable inter- and trans-generational increase in germline apoptosis, aneuploidy, and embryonic lethality. Together, snRNA-seq represents a valuable approach for the detailed examination of an adult organism’s response to environmental exposures.
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•Single-nucleus RNA-seq was used to profile the transcriptome of the adult C. elegans•This approach captured the transcriptome of syncytial tissues such as the germline•snRNA-seq was applied to assess ethanol’s inter- and trans-generational effects•Ethanol transcriptionally and functionally impacts germline homeostasis
Truong et al. apply single-nucleus RNA-seq to profile the transcriptome of the adult C. elegans in response to ethanol exposure across generations. They demonstrate the utility of snRNA-seq for studying the asymmetrical inter- and trans-generational effects of environmental cues on different cell types in C. elegans.
WormBase single-cell tools da Veiga Beltrame, Eduardo; Arnaboldi, Valerio; Sternberg, Paul W
Bioinformatics advances,
2022, Letnik:
2, Številka:
1
Journal Article
Recenzirano
Odprti dostop
We present two web apps for interactively performing common tasks with single-cell RNA sequencing data:
for differential expression and
for visualization of gene expression. We deployed these tools ...with public
datasets curated by WormBase at https://single-cell.wormbase.org. Source code for deploying these tools with other datasets is available at https://github.com/WormBase/scdefg and https://github.com/WormBase/wormcells-viz.
Supplementary data are available at
online.
The construction of physical three-dimensional (3D) models of biomolecules can uniquely contribute to the study of the structure-function relationship. 3D structures are most often perceived using ...the two-dimensional and exclusively visual medium of the computer screen. Converting digital 3D molecular data into real objects enables information to be perceived through an expanded range of human senses, including direct stereoscopic vision, touch, and interaction. Such tangible models facilitate new insights, enable hypothesis testing, and serve as psychological or sensory anchors for conceptual information about the functions of biomolecules. Recent advances in consumer 3D printing technology enable, for the first time, the cost-effective fabrication of high-quality and scientifically accurate models of biomolecules in a variety of molecular representations. However, the optimization of the virtual model and its printing parameters is difficult and time consuming without detailed guidance. Here, we provide a guide on the digital design and physical fabrication of biomolecule models for research and pedagogy using open source or low-cost software and low-cost 3D printers that use fused filament fabrication technology.
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