Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2.
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DOI：
10.1038/s41587-020-0739-1
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发表时间：
2021-03
影响因子：
46.9
通讯作者：
Chen F
中科院分区：
文献类型：
--
作者：
Stickels RR;Murray E;Kumar P;Li J;Marshall JL;Di Bella DJ;Arlotta P;Macosko EZ;Chen F
测量分子在组织中的位置对于理解组织形成和功能是必不可少的。此前，我们开发了Slide-seq，这是一种能够以10 μm的空间分辨率在转录组范围内检测RNA的技术。在这里，我们报告了Slide-seqV 2，它结合了文库生成，珠合成和阵列索引的改进，以达到约50%的单细胞RNA测序数据的RNA捕获效率（比Slide-seq高约10倍），接近基于液滴的单细胞RNA-seq技术的检测效率。首先，我们利用Slide-seqV 2的检测效率来识别小鼠海马神经元中的树突定位mRNA。其次，我们将Slide-seqV 2数据的空间信息与单细胞轨迹分析工具相结合，以表征小鼠新皮层的时空发育，识别Slide-seq采样较差的潜在遗传程序。近细胞分辨率和高转录检测效率的结合使得Slide-seqV 2在许多实验环境中都很有用。
Measurement of the location of molecules in tissues is essential for understanding tissue formation and function. Previously, we developed Slide-seq, a technology that enables transcriptome-wide detection of RNAs with a spatial resolution of 10 μm. Here, we report Slide-seqV2, which combines improvements in library generation, bead synthesis, and array indexing to reach an RNA capture efficiency of ~50% of single cell RNA sequencing data (~10x greater than Slide-seq) approaching the detection efficiency of droplet-based single-cell RNA-seq techniques. First, we leverage the detection efficiency of Slide-seqV2 to identify dendritically localized mRNAs in neurons of the mouse hippocampus. Second, we integrate the spatial information of Slide-seqV2 data with single-cell trajectory analysis tools to characterize the spatiotemporal development of the mouse neocortex, identifying underlying genetic programs that were poorly sampled with the Slide-seq. The combination of near-cellular resolution and high transcript detection efficiency makes Slide-seqV2 useful across many experimental contexts.
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影响因子：
64.8
作者：
Cao, Junyue;Spielmann, Malte;Shendure, Jay
通讯作者：
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DOI：
10.1073/pnas.96.19.10729
发表时间：
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影响因子：
11.1
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通讯作者：
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影响因子：
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