Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis.
Spatiotemporal transcriptomic maps of whole mouse embryos at the onset of organogenesis.
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在器官发生时，整个小鼠胚胎的时空转录组图。
DOI：
10.1038/s41588-023-01435-6
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发表时间：
2023-07
期刊：
影响因子：
30.8
通讯作者：
Meissner, Alexander
中科院分区：
文献类型：
--
作者：
Kumar, Abhishek Sampath;Tian, Luyi;Bolondi, Adriano;Hernandez, Amelia Aragones;Stickels, Robert;Kretzmer, Helene;Murray, Evan;Wittler, Lars;Walther, Maria;Barakat, Gabriel;Haut, Leah;Elkabetz, Yechiel;Macosko, Evan Z.;Guignard, Leo;Chen, Fei;Meissner, Alexander
基因表达的时空协调是胚胎正常发育所必需的。单细胞技术的使用已经开始提供早期调控动力学的改进分辨率，包括小鼠胚胎发生过程中大多数细胞状态的详细分子定义。在这里，我们使用Slide-seq技术构建了完整胚胎日(E) 8.5和E9.0以及部分E9.5胚胎的空间转录组图谱。为了支持他们的应用，我们开发了sc3D，一个重建和探索三维“虚拟胚胎”的工具，它可以定量研究区域化的基因表达模式。我们沿着发育中的神经管的主要胚胎轴的测量揭示了几个以前未注释的具有不同空间模式的基因。我们还描述了在Tbx6突变胚胎中出现的“异位”神经管的相互冲突的转录身份。综上所述，我们提出了一个实验和计算框架，用于整个胚胎结构和突变表型的时空研究。在器官发生开始时（胚胎期8.5-9.5天）对小鼠胚胎进行Slide-seq分析，再加上新的三维重建和可视化工具（sc3D），提供了高分辨率的时空基因表达动态图。
Spatiotemporal orchestration of gene expression is required for proper embryonic development. The use of single-cell technologies has begun to provide improved resolution of early regulatory dynamics, including detailed molecular definitions of most cell states during mouse embryogenesis. Here we used Slide-seq to build spatial transcriptomic maps of complete embryonic day (E) 8.5 and E9.0, and partial E9.5 embryos. To support their utility, we developed sc3D, a tool for reconstructing and exploring three-dimensional ‘virtual embryos’, which enables the quantitative investigation of regionalized gene expression patterns. Our measurements along the main embryonic axes of the developing neural tube revealed several previously unannotated genes with distinct spatial patterns. We also characterized the conflicting transcriptional identity of ‘ectopic’ neural tubes that emerge in Tbx6 mutant embryos. Taken together, we present an experimental and computational framework for the spatiotemporal investigation of whole embryonic structures and mutant phenotypes. Slide-seq profiling of mouse embryos at the onset of organogenesis (embryonic days 8.5–9.5) coupled with a new three-dimensional reconstruction and visualization tool (sc3D) provides high-resolution maps of spatiotemporal gene expression dynamics.
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影响因子：
64.8
作者：
Cao, Junyue;Spielmann, Malte;Shendure, Jay
通讯作者：
Shendure, Jay
影响因子：
4.6
作者：
Delile, Julien;Rayon, Teresa;Sagner, Andreas
通讯作者：
Sagner, Andreas
影响因子：
2.7
作者：
Chapman, DL;Agulnik, I;Papaioannou, VE
通讯作者：
Papaioannou, VE
影响因子：
64.8
作者：
Dickinson ME;Flenniken AM;Ji X;Teboul L;Wong MD;White JK;Meehan TF;Weninger WJ;Westerberg H;Adissu H;Baker CN;Bower L;Brown JM;Caddle LB;Chiani F;Clary D;Cleak J;Daly MJ;Denegre JM;Doe B;Dolan ME;Edie SM;Fuchs H;Gailus-Durner V;Galli A;Gambadoro A;Gallegos J;Guo S;Horner NR;Hsu CW;Johnson SJ;Kalaga S;Keith LC;Lanoue L;Lawson TN;Lek M;Mark M;Marschall S;Mason J;McElwee ML;Newbigging S;Nutter LM;Peterson KA;Ramirez-Solis R;Rowland DJ;Ryder E;Samocha KE;Seavitt JR;Selloum M;Szoke-Kovacs Z;Tamura M;Trainor AG;Tudose I;Wakana S;Warren J;Wendling O;West DB;Wong L;Yoshiki A;International Mouse Phenotyping Consortium;Jackson Laboratory;Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris (ICS);Charles River Laboratories;MRC Harwell;Toronto Centre for Phenogenomics;Wellcome Trust Sanger Institute;RIKEN BioResource Center;MacArthur DG;Tocchini-Valentini GP;Gao X;Flicek P;Bradley A;Skarnes WC;Justice MJ;Parkinson HE;Moore M;Wells S;Braun RE;Svenson KL;de Angelis MH;Herault Y;Mohun T;Mallon AM;Henkelman RM;Brown SD;Adams DJ;Lloyd KC;McKerlie C;Beaudet AL;Bućan M;Murray SA
通讯作者：
Murray SA
影响因子：
2.6
作者：
Chapman, DL;Cooper-Morgan, A;Papaioannou, VE
通讯作者：
Papaioannou, VE