Du Mei R M, Wang Changqing, Law Charity W, Amann-Zalcenstein Daniela, Anttila Casey J A, Ling Ling, Hickey Peter F, Sargeant Callum J, Chen Yunshun, Ioannidis Lisa J, Rajasekhar Pradeep, Yip Raymond K H, Rogers Kelly L, Hansen Diana S, Bowden Rory, Ritchie Matthew E
The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
Department of Medical Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
Genome Biol. 2025 Mar 28;26(1):77. doi: 10.1186/s13059-025-03543-4.
Spatial transcriptomics allows gene expression to be measured within complex tissue contexts. Among the array of spatial capture technologies available is 10x Genomics' Visium platform, a popular method which enables transcriptome-wide profiling of tissue sections. Visium offers a range of sample handling and library construction methods which introduces a need for benchmarking to compare data quality and assess how well the technology can recover expected tissue features and biological signatures.
Here we present SpatialBenchVisium, a unique reference dataset generated from spleen tissue of mice responding to malaria infection spanning several tissue preparation protocols (both fresh frozen and FFPE, with either manual or CytAssist tissue placement). We note better quality control metrics in reference samples prepared using probe-based capture methods, particularly those processed with CytAssist, validating the improvement in data quality produced with the platform. Our analysis of replicate samples extends to explore spatially variable gene detection, the outcomes of clustering and cell deconvolution using matched single-cell RNA-sequencing data and publicly available reference data to identify cell types and tissue regions expected in the spleen. Multi-sample differential expression analysis recovered known gene signatures related to biological sex or gene knockout.
空间转录组学能够在复杂的组织环境中测量基因表达。在现有的一系列空间捕获技术中，10x基因组学公司的Visium平台是一种常用方法，它能够对组织切片进行全转录组分析。Visium提供了一系列样本处理和文库构建方法，这就需要进行基准测试，以比较数据质量，并评估该技术在恢复预期组织特征和生物学特征方面的表现。
在此，我们展示了SpatialBenchVisium，这是一个独特的参考数据集，它来自感染疟疾的小鼠脾脏组织，涵盖了多种组织制备方案（新鲜冷冻和福尔马林固定石蜡包埋，组织放置方式分为手动和使用CytAssist）。我们注意到，使用基于探针的捕获方法制备的参考样本，尤其是经过CytAssist处理的样本，具有更好的质量控制指标，这验证了该平台在数据质量方面的提升。我们对重复样本的分析进一步探索了空间可变基因检测、使用匹配的单细胞RNA测序数据进行聚类和细胞反卷积的结果，以及利用公开可用的参考数据来识别脾脏中预期的细胞类型和组织区域。多样本差异表达分析恢复了与生物性别或基因敲除相关的已知基因特征。
