1Spatiotemporal transcriptional dynamics of cardiac neural crest cellsSource: STOmics DB (ID: STT0000112 )

The contribution of migrating cardiac neural crest cell (CNCC) to the cardiovascular system is a dynamic and finely regulated process. However, the environmental signals influencing when, where, and how CNCCs migrate and begin to differentiate remain to be fully elucidated. In this study, we combined scRNA-seq and scStereo-seq to construct a spatiotemporal atlas of early developmental mouse cardiopharyngeal. We revealed three distinct transition paths and associated biological events during early NCC mesenchymalization, which are related to pre-epithelial-mesenchymal transition and early migration NCCs and their migratory environments. Notably, different transition paths appear to correspond to different downstream fates including CNCC and chondrocyte. Furthermore, we assigned Gata3+ cardiac mesenchymal cells in the pharyngeal region to the Sox10+ migration NCC lineage, categorizing them into distinct subtypes contributing to the outflow tract and pharyngeal arches, and reconstructed their spatiotemporal molecular dynamics of migration and differentiation. Our analysis also indicates that CNCCs migrating to the endocardial cushions and endocardial cells acquired similar mesenchymal fates during early valve development. Additionally, interactions between CNCCs and non-NCC lineage cells facilitated CNCC specification and tissue remodeling. In summary, our study provides new insights into the spatiotemporal lineage evolution and regulatory mechanisms of CNCCs

2comprehensive spatial transcriptomes of C4 grass leaf uncover the molecular mechanisms of morphogenesis of KranzSource: STOmics DB (ID: STT0000093 )

C4 plant evolved convergently from differently lineages of C3 plants, which have higher efficiency of photosynthesis alongside higher water use efficiency and nitrogen use efficiency. Although the process of C4 photosynthesis metabolism are relatively clear, the initiation and morphogenesis of kranz anatomy is largely unclear. Although systems biology approaches have greatly advanced our understanding of C4 photosynthesis regulation, comprehensive genomic spatial transcriptomes of the C4 plant leaf are lacking, which are crucial to fully elucidate the morphogenesis mechanisms of Kranz anatomy. In this study, we utilized spatial enhanced resolution omics-sequencing (Stereo-seq) to develop a spatial transcriptomic atlas of the leaf primordium and also generated a single-nucleus transcriptomic atlas for the early stage. Combination of these spatial and snRNA-seq atlases allow us to use Semi-supervised clustering to sub-cluster and isolate a cluster of very early BSC which could not be identified by unsupervised clustering in scRNA-seq data. By integrating the spatial transcriptomes of Kranz anatomy at the same stage, we constructed a pseudo-Kranz anatomy to elucidate the diffusion expression patterns of key genes within Kranz anatomy. We found that maize SHR and SCR genes are primarily expressed in veins and MC, respectively, and are also notably overlapping in the bundle sheath cells (BSC). We constructed a conserved regulatory network for the C4 plant leaf primordium and identified key TFs that are crucial for C4 Kranz anatomy development, with a particular focus on the significantly elevated expression of SHR genes within the procambium. Among the conserved regulatory network, we validated that IDDP1 and IDD7 are implicated in controlling the morphogenesis of Kranz anatomy, potentially through their interaction with SCR genes. In summary, we established a high-throughput, high-resolution snRNA-seq and spatial transcriptomic atlas for leaf primordia across four grass species, and we have delineated a conserved gene regulatory network governing Kranz anatomy development, which serves as a valuable resource for researchers exploring grass leaf development.

3Public Datasets of STOmicsSource: STOmics DB (ID: STT0000124 )

Browse and obtain STOmics public datasets for further exploration needs.

4Spatiotemporal 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.

5A 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.

6lung 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.

7Integrating 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.

8Reactivation 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.

9Single 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

10The 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.