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 ~50% that of single-cell RNA-seq data (~10-fold 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 Slide-seq. The combination of near-cellular resolution and high transcript detection efficiency makes Slide-seqV2 useful across many experimental contexts.

测量组织中分子的位置对于了解组织的形成和功能至关重要。此前，我们开发了 Slide-seq，这是一种能够以 10 μm 的空间分辨率对转录组范围内的 RNA 进行检测的技术。在这里，我们报告了 Slide-seqV2，它结合了文库生成、珠子合成和阵列索引方面的改进，以达到单细胞 RNA-seq 数据的约 50% 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-seqV2 的检测效率来识别小鼠海马神经元中树突状定位的 mRNA。第二，我们将 Slide-seqV2 数据的空间信息与单细胞轨迹分析工具相结合，以表征小鼠新皮质的时空发育，识别使用 Slide-seq 采样不佳的潜在遗传程序。近细胞分辨率和高转录本检测效率的结合使 Slide-seqV2 在许多实验环境中都很有用。