1Public Datasets of STOmicsSource: STOmics DB (ID: STT0000124 )

Browse and obtain STOmics public datasets for further exploration needs.

2Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolutionSource: STOmics DB (ID: STT0000047 )

Intracerebral hemorrhage (ICH) is a prevalent disease with high mortality. Despite advances in clinical care, the prognosis of ICH remains poor due to an incomplete understanding of the complex pathological processes. To address this challenge, we generated single-cell resolution spatiotemporal transcriptomic maps of mouse brain after ICH. This data set is the most extended resource available that provides detailed information about temporal expression of genes together with a high resolution cellular profile and preserved cellular organization. We identified 100 distinct cellular subclasses, 17 of which were found to play significant roles in the pathophysiology of ICH. We also report similarities and differences between two experimental ICH models and human postmortem ICH brain tissue. This study advances the understanding of the local and global responses of brain cells to ICH, and provides a valuable resource that can facilitate future research and aid the development of novel therapies for this devastating condition.

3A spatially resolved atlas of human breast cancerSource: STOmics DB (ID: STT0000029 )

By integrating Stereo-seq with scRNA-seq data, we established a spatially resolved transcriptomic atlas of human breast cancers across four molecular subtypes, providing a unique resource that comprehensively delineates the ecosystem of primary breast tumors and metastatic lymph nodes.

4lung 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.

5Integrating 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.

6Reactivation 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.

7Single 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

8The 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.

9Spatial 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.

10Spatial 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.