DeST-OT: Alignment of Spatiotemporal Transcriptomics Data.
DeST-OT: Alignment of Spatiotemporal Transcriptomics Data.
复制标题
DeST-OT：时空转录组数据的比对。
DOI：
10.1101/2024.03.05.583575
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发表时间：
2024
期刊：
影响因子：
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通讯作者：
Raphael,BenjaminJ
中科院分区：
文献类型：
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作者：
Halmos,Peter;Liu,Xinhao;Gold,Julian;Chen,Feng;Ding,Li;Raphael,BenjaminJ
空间分辨转录学(SRT)测量组织切片中数千个位置的mRNA转录，揭示基因表达和细胞类型的空间差异。SRT已被应用于生物体发育过程中多个时间点的组织切片。我们介绍了发展时空最优传输(DEST-OT)，这是一种使用最优传输(OT)对齐时空转录数据的方法。DEST-OT使用松弛的OT来模拟细胞的生长、死亡和分化过程。我们还推导了农业扭曲度量和迁徙度量，以量化时空排列的合理性。DeST-OT在对发育中的小鼠肾脏和Axolotl脑的时空转录数据进行比对方面优于现有的方法。DeST-OT估计的增长率还提供了对控制细胞在空间和时间上的生长和分化的基因表达程序的洞察。
Spatially resolved transcriptomics (SRT) measures mRNA transcripts at thousands of locations within a tissue slice, revealing spatial variations in gene expression and cell types. SRT has been applied to tissue slices from multiple time points during the development of an organism. We introduce developmental spatiotemporal optimal transport (DeST-OT), a method to align spatiotemporal transcriptomics data using optimal transport (OT). DeST-OT usessemi-relaxedOT to model cellular growth, death, and differentiation processes. We also derive agrowth distortion metricand amigration metricto quantify the plausibility of spatiotemporal alignments. DeST-OT outperforms existing methods on the alignment of spatiotemporal transcriptomics data from developing mouse kidney and axolotl brain. DeST-OT estimated growth rates also provide insights into the gene expression programs governing the growth and differentiation of cells over space and time.