Size matters: the impact of nucleus size on results from spatial transcriptomics.
Size matters: the impact of nucleus size on results from spatial transcriptomics.
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DOI：
10.1186/s12967-023-04129-z
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发表时间：
2023-04-21
影响因子：
7.4
通讯作者：
Mieczkowski, Jakub
中科院分区：
文献类型：
--
作者：
Mohammadi, Elyas;Chojnowska, Katarzyna;Bienkowski, Michal;Kostecka, Anna;Koczkowska, Magdalena;Zmijewski, Michal A.;Jakalski, Marcin;Ingelsson, Martin;Filipowicz, Natalia;Olszewski, Pawel;Davies, Hanna;Wierzbicka, Justyna M. M.;Hyman, Bradley T. T.;Dumanski, Jan P. P.;Piotrowski, Arkadiusz;Mieczkowski, Jakub
关键词：
Visium空间基因表达（ST）是一种将组织学空间信息与直接来自组织切片的转录组学谱相结合的方法。空间信息的使用使得发现基因表达调控的新模式成为可能。然而，在ST实验中，细胞核的大小可能超过组织切片的厚度。这又可能对在单个切片中全面捕获转录组学谱产生负面影响，特别是对于细胞核大小差异大的组织。在这里，我们定义了连续切片数据集成（CSDI）对揭示人类死后大脑中空间转录组斑点的准确斑点聚类和去卷积的影响。通过考虑组织学信息作为参考，我们评估了CSDI前后无监督聚类和单核RNA-seq和ST数据整合的改进。除了代表神经元层的确定簇数量增加外，连续切片中的簇模式仅在CSDI后一致。此外，分配给点的细胞标记与CSDI后组织切片的组织学模式相匹配。CSDI可以应用于研究在人类大脑皮层中用ST研究的连续切片，避免对斑点聚类和注释的误解，提高细胞识别的准确性以及在揭示人类大脑中灰质层方面的改进。在线版本包含补充材料，可通过10.1186/s12967-023-04129-z获得。
Visium Spatial Gene Expression (ST) is a method combining histological spatial information with transcriptomics profiles directly from tissue sections. The use of spatial information has made it possible to discover new modes of gene expression regulations. However, in the ST experiment, the nucleus size of cells may exceed the thickness of a tissue slice. This may, in turn, negatively affect comprehensive capturing the transcriptomics profile in a single slice, especially for tissues having large differences in the size of nuclei. Here, we defined the effect of Consecutive Slices Data Integration (CSDI) on unveiling accurate spot clustering and deconvolution of spatial transcriptomic spots in human postmortem brains. By considering the histological information as reference, we assessed the improvement of unsupervised clustering and single nuclei RNA-seq and ST data integration before and after CSDI. Apart from the escalated number of defined clusters representing neuronal layers, the pattern of clusters in consecutive sections was concordant only after CSDI. Besides, the assigned cell labels to spots matches the histological pattern of tissue sections after CSDI. CSDI can be applied to investigate consecutive sections studied with ST in the human cerebral cortex, avoiding misinterpretation of spot clustering and annotation, increasing accuracy of cell recognition as well as improvement in uncovering the layers of grey matter in the human brain. The online version contains supplementary material available at 10.1186/s12967-023-04129-z.
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影响因子：
16.2
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Kim EJ;Juavinett AL;Kyubwa EM;Jacobs MW;Callaway EM
通讯作者：
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通讯作者：
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