1A unified spatial transcriptome profiling of ten mouse organsSource: STOmics DB (ID: STT0000184 )

Spatial transcriptomics has enabled numerous deep learning models in this area, and training them requires large amounts of high-quality data, especially expression matrices paired with histological images. Here, we present a unified spatial transcriptomic dataset generated using the Stereo-seq platform, covering 10 mouse organs-including brain, kidney, lung, thymus, large intestine, skin, spleen, ovary, testis, and uterus-encompassing 23 tissue sections generated from 21 chips, each with matched ssDNA or H&E staining images. The dataset comprises single-cell-resolution or square bin-50 expression matrices for each sample, accompanied by corresponding cell type annotations. Annotation robustness was further supported by concordance across different sections of the same tissue and corroboration with canonical marker gene expression patterns. Finally, we compared the characteristics of the cell-bin and bin-50 expression matrices and demonstrated the advantages of cell-bin resolution for cell annotation. This dataset provides a standardized resource for spatial transcriptomics method development, benchmarking, and multimodal analysis.

2Spatiotemporal transcriptome atlas of human embryos after gastrulationSource: STOmics DB (ID: STT0000025 )

Leveraging Stereo-seq technology, we generated spatial transcriptomic profiles across 77 sagittal sections of 13 whole human embryos ranging from Carnegie stage 12 to 23, integrated with single-nucleus RNA-seq to elucidate gene expression patterns within defined cellular contexts, revealing the cellular heterogeneity that drives organ-specific differentiation.

3Multi-omics study of mouse carotid arteriesSource: STOmics DB (ID: STT0000095 )

Advanced atherosclerosis (AS) is the dominant cause of cardiovascular and cerebrovascular events. Tumors may occur during the progression of advanced AS. However, the effect of new-onset tumors on advanced AS remains unclear. Our study demonstrated that individuals (patients and mice) with comorbid advanced AS and cancer exhibited decreased plaque size and enhanced plaque stability. Multiomics analysis revealed that tumors impede advanced AS progression by depriving arginine, suppressing T cell activation, and reducing the secretion of proinflammatory cytokines. Tumor-induced arginine deficiency disrupted the interaction between GPR137B and DDX3X, leading to the mitochondrial translocation of DDX3X. This translocation triggered T cell metabolic reprogramming and subsequent advanced AS suppression. These findings provide new insights into the impact of tumors on advanced AS and can guide the management of patients with coexisting conditions. This work also highlights the potential of targeting T cell GPR137B deletion as a therapeutic strategy for atherosclerotic diseases.

4Persistent chronic inflammation and alveolar bronchiolization in SARS-CoV-2 infected hamsterSource: STOmics DB (ID: STT0000082 )

Persistent chronic inflammation and alveolar bronchiolization in SARS-CoV-2 infected hamster

5Spatial transcriptomics elucidates the central role of cerebral vasculatures in the progression of Japanese encephalitisSource: STOmics DB (ID: STT0000076 )

The molecular mechanisms through which Japanese encephalitis virus (JEV) crosses the BBB and induces encephalitis remain poorly understood. In this study, we employed Stereo-seq technology to conduct a detailed characterization of the spatiotemporal transcriptional dynamics in the mouse brain after JEV infection. We inoculated BALB/c mice with 10^6 PFU of JEV in 200 μl of phosphate-buffered saline (PBS) or 200 μl of PBS in the mock-treated group. On the 3rd, 5th, and 7th day post inoculation (dpi), the mouse brains (n = 3) were collected for Stereo-seq experiment. Our findings reveal the cellular and molecular mechanisms of key pathogenic processes, including viral infection, BBB disruption, immune cell activation and recruitment, and cell death, thereby providing new targets for JE prevention and treatment.

6Spatiotemporal Decoding of Atherosclerosis at Single-Cell ResolutionSource: STOmics DB (ID: STT0000118 )

Atherosclerosis is a spatially and temporally organized disease in which vascular cell identities are reshaped within the constrained architecture of the arterial wall. Yet how spatial context regulates vascular cell state transitions contributing to atherosclerosis progression remains unresolved. Here, we generate a single-cell-resolution spatial transcriptomic atlas of atherosclerosis in mice, anchored in extensive validation from human lesions, comprising ~3 million cells across multiple disease stages and vascular regions. We develop a spatially informed, cross-species framework that reconstructs smooth muscle cell (SMC) migration and transdifferentiation along the intima-adventitia axis. This reveals that loss of PI16 drives SMC-to-fibroblast fate switching, linking defective extracellular matrix remodeling to fibrous-cap destabilization. We further identify hub transcription factors in endothelial cells and SMCs that control early atherogenic remodeling. Together, our study establishes a unified spatial framework for vascular cell plasticity in atherosclerosis with direct translational relevance.

7Spatial transcriptomics combined with sc RNA sequencing reveals pathogenic mechanisms in lupus erythematosus skin lesionsSource: STOmics DB (ID: STT0000149 )

Lupus, a severe and complex autoimmune disease, is clinically divided into cutaneous lupus erythematosus (CLE) which featured in skin damage, and systemic lupus erythematosus (SLE) which characterized in systemic multi-organ damage. However, the characteristics and distinctions of the immune microenvironment in lesions of DLE and SLE patients has not been fully understood. Here, we performed spatial transcriptomic sequencing (Stereo-seq) to characterize cellular infiltration and crosstalk in 15 skin biopsies of healthy control(HC), DLE, and SLE, which providing a comprehensive in-depth knowledge of the nature of lupus skin lesions to guide the development of better treatments.

8HPAH mice's lung Stereo-seqSource: STOmics DB (ID: STT0000179 )

The spatial transcriptomics data of lung tissues of male C57BL/6J mice raised in normoxic condition or in hypoxic condition for 3, 7, 14, 21 or 28 days.

9Spatiotemporal study of hepatitis BSource: STOmics DB (ID: STT0000102 )

Liver cirrhosis and liver cancer caused by hepatitis B virus infection cause about 800000 deaths every year. In this study, we used Stereo-seq FFPE technology to obtain the transcriptome of liver biopsy tissues from 11 hepatitis B patients and 3 normal controls, identifying disease progression markers in each stage of hepatitis B virus infection.

10Spatiotemporal transcriptome of potato-phytophthora infestans interactionSource: STOmics DB (ID: STT0000143 )

To investigate the dynamic transcriptional reprogramming in potato leaves during early stages of P. infestans infection, we collected leaf samples from diploid potato A6-26 plants that were inoculated with P. infestans strain 88069td at 3 hours post-infection (hpi), 6 hpi, 12 hpi and 24 hpi. We retrieve the major cell types of potato leaves and elucidate the cell-type-specific gene expression patterns. We further distinguish cells that are directly targeted by pathogen.