1Spatiotemporal 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.

2Spatial 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.

3HPAH 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.

4Spatiotemporal 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.

5Spatiotemporal 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.

6Spatial 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.

7spatiotemporal transcriptomes of maize leaf at early stagesSource: STOmics DB (ID: STT0000121 )

Here, we constructed single cell spatial transcriptomes and single cell RNA-seq (scRNA-seq) atlases of leaf primordia for maize (Zea mays). By integrating spatial and scRNA-seq data in maize, we identified all cell types, particularly bundle sheath cells (BSC) at early developmental stages. We developed a unified pseudo-Kranz framework to integrate transcriptomics data for cells at different positions and distances from vascular bundles. We construct genetic regulatory networks for different cell types in early developing leaves and consequently identified newly recruited regulators related to Kranz anatomy.

8wing primordium of the domestic silkwormSource: STOmics DB (ID: STT0000176 )

scRNA-seq data in the wing primordium of the domestic silkworm during normal development at 5th instar, 2nd day; 5th instar, 3rd day; 5th instar, 4th day; 5th instar, 5th day; 5th instar, 6th day; 5th instar, 7th day; WD period, 1st day; WD period, 2nd day; and P period. snRNA-seq data in the wing primordium of the domestic silkworm after hormonal induction treatment following normal development until 5th instar, 2nd day; 0h; 10 min; 20 min; 30 min; 40 min; 50 min; 60 min; 4h; and 6h. stereo-seq data of single cells in the wing primordium of the domestic silkworm during normal development at 5th instar, 2nd day; 5th instar, 3rd day; and WD period, 2nd day.

9Exploring the mechanism of tumer microenvironment reconstruction in the process of breast cancer invasionSource: STOmics DB (ID: STT0000067 )

Breast cancer is a leading cause of death that seriously threatens women's life and health. Tumor invasion is a crucial event in the progression of breast cancer. However, we still know little about the specific mechanisms of tumor invasion in breast cancer. In this study, we perform single-cell and spatial RNA-sequencing on tumor samples from normal, in situ and invasive regions to explore the specific cellular and molecular mechanisms of the dynamic tumor microenvironment reconstruction during tumor invasion, thus providing new targets for clinical diagnosis and treatment of breast cancer.

10Single-cell and spatial transcriptomics reveal the mechanisms of bile duct injury in biliary atresiaSource: STOmics DB (ID: STT0000060 )

Biliary Atresia(BA) is a devastating pediatric cholangiopathy affecting the bile ducts of the liver. This research utilized spatial and single-cell transcriptomics to analyze the immune microenvironment of biliary atresia, revealing the mechanisms of bile duct injury that occur concurrently with inflammation and fibrosis.