VISTA: Visualizing the Spatial Transcriptome of the C. elegans Nervous System.
VISTA: Visualizing the Spatial Transcriptome of the C. elegans Nervous System.
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VISTA：可视化线虫神经系统的空间转录组。
DOI：
10.1101/2023.04.28.538711
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发表时间：
2023
期刊：
影响因子：
--
通讯作者：
Norris,Adam
中科院分区：
文献类型：
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作者：
Liska,David;Wolfe,Zachery;Norris,Adam
在不牺牲空间信息的情况下分析单细胞的转录组是空间转录组学领域的主要目标，但目前的技术需要在单细胞分辨率和全转录组覆盖之间进行权衡。在一种动物物种——秀丽隐杆线虫（caenorhabditis elegans）中，利用现有的数据集，可以获得具有单细胞分辨率的综合空间转录组，这要归功于蠕虫不变的细胞谱系和一系列最近生成的单细胞转录组。在这里，我们提出了VISTA，它利用这些数据集来提供蠕虫空间转录组的可视化，特别关注神经系统。VISTA允许用户输入查询基因，并以“空间热图”的形式将其在所有神经元中的表达可视化，其中细胞的颜色报告了表达水平。当选择单个细胞时，显示潜在的基因表达值（每百万转录本）。我们提供了VISTA在识别特定神经元中引人注目的新基因表达模式以及解决由活体报告基因产生的模糊表达模式的细胞身份方面的应用实例。容易获得神经元空间转录组的基因水平快照的能力将有助于神经元特异性基因表达和调控的研究，并为该领域希望在未来获得各种动物物种的高分辨率空间转录组提供模板。可用性和实现vista可在以下网址免费获得：https://public.tableau.com/app/profile/smu.oit.data.insights/viz/VISTA_16814210566130/VISTA。
SummaryProfiling the transcriptomes of single cells without sacrificing spatial information is a major goal of the field of spatial transcriptomics, but current technologies require tradeoffs between single-cell resolution and whole-transcriptome coverage. In one animal species, the nematode wormCaenorhabditis elegans, a comprehensive spatial transcriptome with single-cell resolution is attainable using existing datasets, thanks to the worm’s invariant cell lineage and a series of recently generated single cell transcriptomes. Here we present VISTA, which leverages these datasets to provide a visualization of the worm spatial transcriptome, focusing specifically on the nervous system. VISTA allows users to input a query gene and visualize its expression across all neurons in the form of a “spatial heatmap” in which the color of a cell reports the expression level. Underlying gene expression values (in Transcripts Per Million) are displayed when an individual cell is selected. We provide examples of the utility of VISTA for identifying striking new gene expression patterns in specific neurons, and for resolving cellular identities of ambiguous expression patterns generated fromin vivoreporter genes. The ability to easily obtain gene-level snapshots of the neuronal spatial transcriptome should facilitate studies on neuron-specific gene expression and regulation and provide a template for the high-resolution spatial transcriptomes the field hopes to obtain for various animal species in the future.Availability and implementationVISTA is freely available at the following URL: https://public.tableau.com/app/profile/smu.oit.data.insights/viz/VISTA_16814210566130/VISTA.