Bioinformatics Seminars

Bioinformatics Seminar

Time: 11AM
Venue: Hybrid

12 September 2023

Sequencing-based Spatial Transcriptomic Methods: From Biology to Technology

Luyi Tian
Guangzhou National Lab

Sequencing-based spatial transcriptomic techniques have experienced rapid advancements in recent years, enabling unbiased, transcriptome-scale measurements of spatial gene expression. In this talk, we present recently published work on the construction of spatial transcriptomic maps for complete embryonic days (E) 8.5 and E9.0, as well as partial E9.5 embryos. We also demonstrate the utility of these maps for elucidating the perturbed transcriptional identities of 'ectopic' neural tubes observed in Tbx6 mutant embryos. Beyond biological applications, the technological advancements in this field are equally compelling. However, these methods have yet to be systematically benchmarked, and the considerable variability across technologies and datasets complicates the establishment of evaluation standards. To address this, our team has developed a set of reference tissues with well-defined histological structures, utilizing them to generate data and assess six distinct technologies. Despite variations in resolution, capture efficiency, and spatial precision, spatial transcriptomic data exhibit characteristics distinct from single-cell RNAseq data, such as enhanced capabilities for capturing rare and spatially patterned cell states, along with more pronounced ambient RNA contamination. This study aims not only to guide biologists in method selection but also to build a consensus on evaluation criteria, establish a framework for future benchmarking, and provide gold standards for the assessment of computational tools.


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