1lung ischemia reperfusion injurySource: STOmics DB (ID: STT0000079 )

Neutrophil extracellular traps formed during lung ischemia reperfusion injury via promotion of CD177+ cells with activated oxidative phosphorylation complex I.

2Integrating single-cell and spatial transcriptomics to illuminate cellular and molecular dynamics of sepsisSource: STOmics DB (ID: STT0000075 )

Septic encephalopathy, recognized for its considerable morbidity and mortality rates, poses a substantial challenge in understanding its pathogenesis. This study utilized a murine model where lipopolysaccharide (LPS) was intraperitoneally administered to both wild type and Anxa1-/- mice. Employing single-cell sequencing and Stereo-seq technology, we analyzed brain tissues at multiple time points post-LPS injection to elucidate the dynamic cellular and molecular responses. Our findings revealed a time-dependent increase in activated glial cells and perivascular aggregation, along with the upregulation of specific receptor ligands following LPS administration. This temporal pattern underscores the dynamic nature of the inflammatory response in septic encephalopathy, irrespective of the presence of the Anxa1. Conversely, Anxa1-/- mice resulted in an earlier decrease in activated astrocytes and receptor ligands compared to wild type mice. These results highlight the pivotal role of temporal changes in driving the disease progression, with the effects of Anxa1 deletion manifesting in a nuanced manner.

3Reactivation of mammalian regeneration by turning back an evolutionarily modified genetic switchSource: STOmics DB (ID: STT0000077 )

The causative genetic changes responsible for the loss of regeneration during mammalian evolution remain elusive. Comparative single-cell sequencing and spatial transcriptomic analyses of rabbits and mice uncovered the suppression of retinoic acid (RA) production, caused by the loss of Aldh1a2 expression and boosted RA degradation, is responsible for the failure of mouse ear pinna regeneration. Reactivation of Aldh1a2 or exogenous supplement of RA but not the synthetic precursor retinol was sufficient to switch the ear pinna repair into complete regeneration. The in vivo lineage tracing showed the restored regeneration was contributed by injury-activated Tnn+ cells. Transgenic reporter assays and a high-resolution map of 3D genome organization revealed evolutionary loss of the AE1 enhancer and injury responsiveness of Aldha1a2 promoter in mice contributed to the difficiencty of Aldh1a2 upon injury. Our study has important implications for dissecting the causative molecular mechanisms responsible for the limited regeneration in damaged human organs.

4Public Datasets of STOmicsSource: STOmics DB (ID: STT0000124 )

Browse and obtain STOmics public datasets for further exploration needs.

5Single Cell Multi-Omic reveal the impact of salt stress on NHCC root tip developmentSource: STOmics DB (ID: STT0000066 )

Single Cell Multi-Omic reveal the impact of salt stress on NHCC root tip development

6The Spatial Transcriptomics of upland rice rootSource: STOmics DB (ID: STT0000026 )

Upland rice and irrigated rice have different root patterning adapted to rainfall or irrigated conditions, respectively. Due to the increasing scarcity of water for irrigation, it is necessary to study the mechanism of root patterning in upland rice. Here we investigated the fine difference in root between these two ecotypes and found that upland rice have less crown root (CR), longer meristem and more cortex in root tip than irrigated rice. We used a high-resolution spatial transcriptomics technology, Stereo-seq, to dissect the transcriptional differences in the CR-producing coleoptile and root tips.

7Spatial transcriptomic study of alveolar echinococcosisSource: STOmics DB (ID: STT0000072 )

Alveolar echinococcosis (AE) is characterized by increased infiltration of various immune cells around the lesion. To investigate the spatial transcriptional dynamics in AE lesions, we conducted Stereo-seq to generate the spatiotemporal transcriptomic atlas of mouse livers collected at multiple timepoints after Echinococcus multilocularis infection.

8Spatial transcriptome sequencing of human early tooth developmentSource: STOmics DB (ID: STT0000140 )

Spatial transcriptome seguencing of human early tooth development at late bud, cap and early bell stages.

9Spatiotemporal transcriptomic atlas of atherosclerosis revealed Smooth muscle cells induce tertiary lymphoid organs in plaqueSource: STOmics DB (ID: STT0000052 )

Tertiary lymphoid organs (TLOs) develop within nonlymphoid tissues in response to persistent inflammation, However, there is limited knowledge regarding their presence in atherosclerosis diseases and the mechanisms underlying their development. Here, we used single-cell RNA sequencing and Spatial Enhanced Resolution Omics-sequencing (Stereo-seq) to obtain a comprehensive plaque atlas comprising 30 distinct transcriptome-defined cell types. Notably, we have observed the presence of TLOs within plaques, and their formation is closely associated with the expression of the lymphorganogenic chemokine, CXCL12, produced by fibroblast-like smooth muscle cells (SMCs) in a LTβR-dependent manner. In plaque TLOs (PTLOs), B cells were abundant and capable of differentiating into IgA- and IgG- plasma cells. BCR repertoire analysis unveiled clonal diversification, selection, expansion in PTLO, and the presence of identical B cell clonotypes in other regions of the plaques. Interestingly, we also identified the co-occurrence of unique B cell clonotypes in plaques and perivascular adipose tissue (PVAT) by using lineage analysis, indicating cell exchange between these compartments. PTLO-derived IgG antibodies promote the differentiation macrophages into foam cells, suggestive of pro-atherogenic effector activity. Additionally, the presence of PTLOs is linked with cardiovascular events. Thus, the PTLOs induced by fibroblast-like SMCs play key roles in the development and stability of atherosclerosis plaques, by conferring B cell maturation and IgG antibody production.

10A Spatiotemporal Dynamic Immune Landscape of the COVID-19 Hamster Lung [Spatiotemporal]Source: STOmics DB (ID: STT0000006 )

Although SARS‐CoV‐2‐mediated inflammation has attracted global health concerns since 2019, its pulmonary immunopathology is not fully understood. Here we generated a comprehensive cellular and molecular landscape of healthy and COVID-19 hamster lungs at different timepoints after infection, using single-cell RNA sequencing and spatial transcriptomic sequencing to map the entire progression of COVID-19. We found SARS-CoV-2 could infect naïve T cells and induced cell death to decrease T cell number at the early stage of COVID-19. Besides, we observed the activation and depletion of tissue resident myeloid cells after infection, the accumulation of Isg12+Cst7+ neutrophils and Il10+Spp1+ M2-like macrophages to clean up virus and resolve inflammation. Finally, we identified Trem2+AM and Fbp1+AM subsets during the resolution stage of COVID-19. Our study provided spatiotemporally-resolved insights into the lung cells transcriptome, identified distinct tissue regions of viral infection, lung injury, repair and remodeling.