Xenium dataset

We developed a method that utilizes floating mounting of thin sections of fixed frozen mouse lung tissue onto Xenium slides for the fluorescent in situ hybridization (FISH) and imaging –based spatial transcriptomics analysis of gene expression using the Xenium platform provided by 10X Genomics. Spatial transcriptomics techniques provide a comprehensive view by merging gene expression data with spatial context within their native tissue architecture. However, the Xenium pipeline has been validated only for formalin-fixed paraffin-embedded (FFPE) and fresh frozen sections by 10X Genomics. Notably, many researchers prefer paraformaldehyde-fixed cryosections for immunohistochemistry and in situ hybridization. In our study, we assessed the compatibility of standard fixed frozen mouse lung sections with the Xenium protocol. Our findings reveal that these sections not only align well with the Xenium platform but also offer superb imaging and gene expression quantification, even with limited number of genes in the Xenium panel. This protocol can serve as a valuable resource for preparing various tissues where FFPE and fresh frozen samples present challenges.

我们开发了一种方法，将固定冷冻的小鼠肺组织薄切片通过悬浮式贴片（floating mounting）固定于Xenium载玻片上，借助10X Genomics推出的Xenium平台开展基于荧光原位杂交（fluorescent in situ hybridization, FISH）与成像的基因表达空间转录组分析。空间转录组技术（spatial transcriptomics）通过将基因表达数据与其天然组织架构内的空间位置信息相结合，可提供全面的组织观测视角。然而，10X Genomics仅针对福尔马林固定石蜡包埋（formalin-fixed paraffin-embedded, FFPE）样本与新鲜冷冻组织切片完成了Xenium实验流程的验证。值得注意的是，诸多研究者更倾向于使用多聚甲醛固定的冷冻切片开展免疫组化与原位杂交实验。本研究中，我们评估了标准固定冷冻小鼠肺组织切片与Xenium实验方案的兼容性。研究结果显示，此类切片不仅可完美适配Xenium平台，还可实现优异的成像效果与基因表达定量分析，即便在Xenium探针组（Xenium panel）覆盖基因数量有限的情况下亦是如此。该实验方案可为那些难以获取FFPE样本与新鲜冷冻样本的多种组织的样本制备工作提供宝贵参考。