Size matters: the impact of nucleus size on results from spatial transcriptomics.

ABSTRACT:

Background

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.

Methods

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 inform

SUBMITTER: Mohammadi E 

PROVIDER: S-EPMC10120157 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature