Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, The Netherlands.
Nat Protoc. 2018 Nov;13(11):2501-2534. doi: 10.1038/s41596-018-0045-2.
Spatial resolution of gene expression enables gene expression events to be pinpointed to a specific location in biological tissue. Spatially resolved gene expression in tissue sections is traditionally analyzed using immunohistochemistry (IHC) or in situ hybridization (ISH). These technologies are invaluable tools for pathologists and molecular biologists; however, their throughput is limited to the analysis of only a few genes at a time. Recent advances in RNA sequencing (RNA-seq) have made it possible to obtain unbiased high-throughput gene expression data in bulk. Spatial Transcriptomics combines the benefits of traditional spatially resolved technologies with the massive throughput of RNA-seq. Here, we present a protocol describing how to apply the Spatial Transcriptomics technology to mammalian tissue. This protocol combines histological staining and spatially resolved RNA-seq data from intact tissue sections. Once suitable tissue-specific conditions have been established, library construction and sequencing can be completed in ~5-6 d. Data processing takes a few hours, with the exact timing dependent on the sequencing depth. Our method requires no special instruments and can be performed in any laboratory with access to a cryostat, microscope and next-generation sequencing.
基因表达的空间分辨率使基因表达事件能够精确定位到生物组织的特定位置。组织切片中的空间分辨基因表达传统上使用免疫组织化学（IHC）或原位杂交（ISH）进行分析。这些技术是病理学家和分子生物学家的宝贵工具；然而，它们的通量限制了一次只能分析少数几个基因。RNA 测序（RNA-seq）的最新进展使得在大量样本中获得无偏的高通量基因表达数据成为可能。空间转录组学将传统的空间分辨技术的优势与 RNA-seq 的大规模通量相结合。在这里，我们介绍了一种应用于哺乳动物组织的空间转录组学技术的方案。该方案结合了完整组织切片的组织学染色和空间分辨 RNA-seq 数据。一旦建立了合适的组织特异性条件，文库构建和测序可以在 5-6 天内完成。数据处理需要几个小时，具体时间取决于测序深度。我们的方法不需要特殊仪器，任何有冷冻切片机、显微镜和下一代测序仪的实验室都可以进行。
