1A 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.

BGI Stereomics Stereo-Seq
Mesocricetus auratus
Sample: 15
Tissue Section: 15

2Hypoxia 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.

BGI Stereomics Stereo-Seq
Mus musculus
Sample: 2
Tissue Section: 2

3A 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.

BGI Stereomics Stereo-Seq
Homo sapiens
Sample: 5
Tissue Section: 44

4Spatial transcriptomic data of Oryza longistaminata rhizomeSource: STOmics DB (ID: STT0000024 )

Spatial transcriptomic data of Oryza longistaminata rhizome

BGI Stereomics Stereo-Seq
Oryza longistaminata
Sample: 10
Tissue Section: 21

5Integrating 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.

BGI Stereomics Stereo-Seq
Homo sapiens
Sample: 2
Tissue Section: 2

6Spatial 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.

BGI Stereomics Stereo-Seq
Mus musculus
Sample: 4
Tissue Section: 4

7test-2022-0829v1.0.0-titleSource: STOmics DB (ID: STT0000001 )

test-2022-0829v1.0.0-sum

BGI Stereomics Stereo-Seq
Homo sapiens
Pseudomonas chlororaphis subsp. chlororaphis
Sample: 2
Tissue Section: 6

8Spatial 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.

BGI Stereomics Stereo-Seq
Lotus japonicus
Sample: 4
Tissue Section: 72

9An 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.

BGI Stereomics Stereo-Seq
Danio rerio
Sample: 9
Tissue Section: 46

10Reconstructing the Evolution of the Mammalian and Avian Telencephalon through Spatial Molecular ArchitectureSource: STOmics DB (ID: STT0000081 )

The evolution of amniotes heralded the emergence of intricate brain organization, particularly in the telencephalon, but its genoarchitectonic identity and evolutionary trajectory remain enigmatic. By constructing spatial transcriptomic atlases of the zebra finch and turtle telencephalon, we enable unparalleled comparisons among sauropsids (reptiles and birds), extending to amphibians (axolotls) and mammals (mice and macaques) allowing us to decipher the evolutionary origins of the complex DVR subregions in birds. We uncovered two divergent gene regulatory models during the evolution of the amniote telencephalon: the 'coupled model', characterized by a conserved regulatory relationship between transcription factors (TFs) and effector genes across species, and the 'shift model', where this regulatory relationship varies across species. Notably, we deciphered the molecular mechanism by which the avian DVR and mammalian neocortex recruit the same effector genes via divergent transcription factors, underscoring their convergent evolution. Collectively, our data shed light on the nuanced evolutionary relationships within the telencephalon among amniote lineages, providing a new fundamental understanding of brain evolution.

BGI Stereomics Stereo-Seq
Pelodiscus sinensis
Taeniopygia guttata
Mus musculus
Sample: 8
Tissue Section: 8