1Single-cell and spatiotemporal transcriptomic reveals the effects of microorganisms on immunity and metabolism in mouse liverSource: STOmics DB (ID: STT0000034 )

The gut-liver axis is a complex bidirectional communication pathway between the intestine and the liver in which microorganisms and their metabolites from the intestine flow through the portal vein to the liver and influence liver function. In a sterile environment, the phenotype or function of the liver is altered, yet there are few studies on the specific cellular and molecular effects of microorganisms on the liver. Towards this aim, we constructed single-cell and spatial transcriptomic (ST) profiles of germ-free (GF) and specific pathogen-free (SPF) mice livers. The single cell RNA sequencing (scRNA-seq) found that the proportion of the vast majority of immune cells in GF mice was significantly reduced, especially natural killer T (NKT) cells, IgA plasma cells (IgAs), and Kupffer cells (KCs). The spatial enhanced resolution omics-sequencing (Stereo-seq) confirmed that microorganisms mediated the accumulation of Kupffer cells in the periportal zone. We also unexpectedly found that IgA plasma cells were more numerous and concentrated in the periportal vein in sections from SPF mice, while they were fewer and scattered in GF mice. ST technology also enables precise zonation of liver lobules into eight layers and three patterns based on gene expression level in each layer, allowing us to further investigate the effects of microbes on gene zonation patterns and functions. Furthermore, the untargeted metabolism experiments in the liver discovered that propionic acid levels were significantly lower in GF mice and may be related to the control of genes involved in bile acid and fatty acid metabolism. In conclusion, the combined study of scRNA-seq, Stereo-seq, and untargeted metabolomics revealed immune system defects as well as altered bile acid and lipid metabolic processes at the single-cell and spatial levels in the livers of GF mice. This study has great value for understanding host-microbiota interactions.

2A 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.

3Hypoxia induced cellular changes in multiple organs and a novel immunoregulatory cell type in spleenSource: STOmics DB (ID: STT0000005 )

Hypoxia is an important physiological stress causing organ injuries and diseases, but 30 its cellular and olecular impacts across organs were not fully understood. We constructed a single-cell spatiotemporal transcriptome atlas of hypoxia, with 350,979 cells from 99 cell clusters. Utilizing this atlas, we depicted hypoxia induced common cell changes including increase of erythroid cells and drastic changes of immune cells. And we found three major gene groups responding to hypoxia, including hypoxia-inducible factors (HIFs), hemoglobin genes, 35 and electron transport chain (ETC) genes. We also found many disease risk genes to be differentially expressed in multiple organs during hypoxia. Finally, we found a hypoxia induced novel cell type in the spleen, defined as erythroid-derived immunoregulatory cells (EDICs). Our dataset and analysis provided new insights into molecular mechanisms and physiological consequences of hypoxia.

4A cellular resolution spatial transcriptomic landscape of the adult human cortexSource: STOmics DB (ID: STT0000059 )

In our pursuit of creating a comprehensive human cortical atlas to understand human intelligence, we examined the single-nuclei transcriptomes of 307,738 cells alongside spatial transcriptomics data from 46,948 VISIUM spots and 1,355,582 Stereo cells. Atlases reveal distinct expression patterns and spatial arrangements of cortical neural cell types. Glutamatergic neurons exhibit precise laminar patterns, often mirroring expression patterns in adjacent cortical regions. Overlaying our atlas with functional networks delineated substantial correlations between neural cell types and cortical region function. Notably, regions involved in processing sensory information (pain) display a pronounced accumulation of extratelencephalic neurons. Additionally, our atlas enabled precise localization of the thicker layer 4 of the visual cortex and an in-depth study of the stabilized subplate structure, known as layer 6b, revealed specific marker genes and cellular compositions. Collectively, our research sheds light on the cellular foundations of the intricate and intelligent regions within the human cortex. The visualization is on https://db.cngb.org/stomics/datasets/STDS0000242.

5Spatial transcriptomic data of Oryza longistaminata rhizomeSource: STOmics DB (ID: STT0000024 )

Spatial transcriptomic data of Oryza longistaminata rhizome

6Integrating Single-Cell RNA Sequencing and Spatial Transcriptomics to Map DEGs in AD Across Key Brain RegionsSource: STOmics DB (ID: STT0000099 )

In Alzheimer's disease (AD) research, understanding the spatial distribution of differentially expressed genes (DEGs) within key brain regions is crucial for elucidating disease mechanisms and identifying potential therapeutic targets. In this study, we utilized physiological group chips to integrate single-cell RNA sequencing (scRNA-seq) data with spatial transcriptomics to map DEGs in two critical brain regions: the dorsolateral prefrontal cortex (DLPFC) and the superior temporal gyrus (STG). By combining these advanced technologies, we aimed to observe the spatial arrangement of DEGs in cortical slices, providing insights into the cellular and molecular landscape of AD progression.

7Spatial transcriptomic data of mouse tissueSource: STOmics DB (ID: STT0000087 )

The raw data contains information on ovarian samples and other non-related samples to this study.

8test-2022-0829v1.0.0-titleSource: STOmics DB (ID: STT0000001 )

test-2022-0829v1.0.0-sum

9Spatial Transcriptomics of Lotus japonicus Nodule OrganogenesisSource: STOmics DB (ID: STT0000041 )

Legumes, such as Lotus japonicus, can gain symbiotic nitrogen fixation ability by forming root nodules. Previous research has shown that these plants do not possess a unique gene family for nodulation, and instead, it is achieved by recruiting genes from other organogenesis pathways. Therefore, understanding the expression sites of genes is crucial in studying nodulation. To investigate determinate nodule organogenesis, we used Stereo-seq to capture spatial transcriptomes on the nodules of L. japonicus. Our study identified key tissue types, at different developmental stages, and characterized them at the molecular level. We determined that the infected zone is distinctive from other tissues, mainly due to the symbiosis, and revealed its coordinate development with the surrounding peripheral tissues. Our analysis discovered several candidate genes involved in nodulation, some of which are likely recruited from root organogenesis. Specifically, we investigated LjNLP3, a member of the NIN-LIKE PROTEIN family, which is highly expressed at a late developmental stage. Functional studies revealed a dual role for LjNLP3 in braking nodule development and promoting maturation, thereby enhancing our understanding of this critical family's functions in nodulation. In summary, our spatiotemporal transcriptomic atlas of L. japonicus nodules provides valuable insights into the molecular mechanisms and functional genes involved in nodulation.

10An Organ-wide Spatiotemporal Transcriptomic Atlas of Regenerating Zebrafish HeartSource: STOmics DB (ID: STT0000071 )

Adult zebrafish robustly regenerate injured hearts through a complex orchestration of cells and molecules. However, the comprehensive process remains incompletely understood. Here, we utilized single-cell RNA-sequencing (scRNA-seq) and Stereo-seq approaches to generate a spatially-resolved cell dataset of regenerating zebrafish heart. We captured organ-scale cellular dynamics across eight time points, with a particular focus on the initiative stages. We deciphered the cellular origin and cascade of regenerating cardiomyocytes, identifying tpm4a as a key player in the re-differentiation of post-proliferated cardiomyocytes. We observed that the activation of lumican in proregenerative fibroblasts is conserved across regenerative hearts of diverse species. In addition, we reconstructed a 4D "virtual regenerating heart" atlas, encompassing 3 spatial dimensions and time, comprising a total of 582,068 cells/spots derived from 36 scRNA-seq libraries and 224 Stereo-seq slices. In summary, our work establishes a foundation framework for future study of cellular dynamics and molecular mechanisms underlying vertebrate heart regeneration.