Genome-wide RNA Tomography in the Zebrafish Embryo
Genome-wide RNA Tomography in the Zebrafish Embryo
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DOI：
10.1016/j.cell.2014.09.038
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发表时间：
2014-10-23
期刊：
影响因子：
64.5
通讯作者：
van Oudenaarden, Alexander
中科院分区：
文献类型：
--
作者：
Junker, Jan Philipp;Noel, Emily S.;van Oudenaarden, Alexander
推进我们对胚胎发育的理解在很大程度上取决于新途径或调节剂的鉴定。虽然全基因组技术如RNA测序非常适合发现新的候选基因，但它们无法在胚胎或组织中产生空间分辨的信息。例如，使用原位杂交的基于显微镜的方法可以提供关于基因表达的空间信息，但仅限于一次分析一个或几个基因。在这里，我们提出了一种方法，我们结合联合收割机传统的组织学技术与低输入的RNA测序和数学图像重建，以产生一个高分辨率的全基因组的三维图谱的基因表达在斑马鱼胚胎在三个发育阶段。重要的是，我们的技术能够搜索在特定空间模式中表达的基因，而无需手动图像注释。我们设想广泛的适用性RNA断层扫描作为一个准确和敏感的方法，在整个胚胎和解剖器官的空间分辨转录。
Advancing our understanding of embryonic development is heavily dependent on identification of novel pathways or regulators. Although genome-wide techniques such as RNA sequencing are ideally suited for discovering novel candidate genes, they are unable to yield spatially resolved information in embryos or tissues. Microscopy-based approaches, using in situ hybridization, for example, can provide spatial information about gene expression, but are limited to analyzing one or a few genes at a time. Here, we present a method where we combine traditional histological techniques with low-input RNA sequencing and mathematical image reconstruction to generate a high-resolution genome-wide 3D atlas of gene expression in the zebrafish embryo at three developmental stages. Importantly, our technique enables searching for genes that are expressed in specific spatial patterns without manual image annotation. We envision broad applicability of RNA tomography as an accurate and sensitive approach for spatially resolved transcriptomics in whole embryos and dissected organs.