Luli S. Zou, Dylan M. Cable, Irving A. Barrera-Lopez, Tongtong Zhao, Evan Murray, Martin J. Aryee, Fei Chen, Rafael A. Irizarry
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引用次数: 0
摘要
空间转录组学技术可以在全基因组范围内以接近单细胞的分辨率研究 RNA 的空间分布。然而,从这些数据中研究空间等位基因特异性表达(ASE)的可行性仍未定性。在这里,我们介绍了用于检测和估计空间等位基因特异性表达的计算框架 spASE。为了应对细胞类型混合物和低信噪比带来的挑战,我们实施了一个涉及空间平滑样条的加性混合物的分层模型。我们将我们的方法应用于小鼠小脑和海马的等位基因分辨 Visium 和 Slide-seq,并报告了对其中空间和细胞类型特异性 ASE 的新见解。
Detection of allele-specific expression in spatial transcriptomics with spASE
Spatial transcriptomics technologies permit the study of the spatial distribution of RNA at near-single-cell resolution genome-wide. However, the feasibility of studying spatial allele-specific expression (ASE) from these data remains uncharacterized. Here, we introduce spASE, a computational framework for detecting and estimating spatial ASE. To tackle the challenges presented by cell type mixtures and a low signal to noise ratio, we implement a hierarchical model involving additive mixtures of spatial smoothing splines. We apply our method to allele-resolved Visium and Slide-seq from the mouse cerebellum and hippocampus and report new insight into the landscape of spatial and cell type-specific ASE therein.
Genome BiologyBiochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍:
Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens.
With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category.
Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.