1Spatial 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.

2Spatial 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.

3An 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.

4Reconstructing 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.

5Spatiotemporal transcriptomic landscape of rice embryonic cells during seed germinationSource: STOmics DB (ID: STT0000049 )

Characterizing cell features of germinating seeds is essential for understanding the complex biological functions of different embryonic cells in regulating seed vigor and seedling establishment. In this study, we performed spatially enhanced resolution omics (Stereo-seq) and single-cell RNA sequencing (scRNA-seq) to capture spatially resolved single-cell transcriptomes of germinating rice embryos. An automated cell-segmentation model was developed based on deep-learning to accommodate the analysis requirements. The spatial transcriptome revealed known and novel cell types of rice embryo, including two new scutellum cell types. The temporal transcriptome revealed the expression dynamics of genes in different types of embryonic cells during the time course of seed germination and the key genes, particularly related to nutrient metabolism and biosynthesis and signaling of phytohormonesand were reprogrammed in a cell-type-specific manner. Our study provides a panoramic spatiotemporal transcriptome of rice embryo and a novel methodology for exploring the roles of different embryonic cells in seed germination.

6A 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.

7Mouse Heart spatial transcriptomeSource: STOmics DB (ID: STT0000009 )

The spatial transcriptomic data of mouse heart

8Fate Determination of Cancer-associated Fibroblast Drives Polarized Immunity in Cancer-stroma BoundarySource: STOmics DB (ID: STT0000036 )

The exciting responding rate to anti-PD1 treatment makes dMMR colorectal cancer (CRC) an outstanding model to explore the mechanism underlying immunotherapy sensitivity. This study provides a spatial transcriptomic landscape of CRC tumor at 50 μm resolution and highlights the plasticity of the cancer-stroma boundary immunity. It demonstrates the utility of high-resolution spatial transcriptome to study the cellular components and molecular pattern in the microscopic boundary, in which cancer cells co-opt stromal cells to alter the boundary immunity.

9The Single-cell Stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leavesSource: STOmics DB (ID: STT0000023 )

Understanding the complex functions of plant leaves requires a thorough characterization of discrete cell features. Although single-cell gene expression profiling technologies have been developed, their application in characterizing cell subtypes has not been achieved yet. Here, we present scStereo-seq (single-cell SpaTial Enhanced REsolution Omics-sequencing) that enabled us to firstly show the bona fide single-cell spatial transcriptome profiles of Arabidopsis leaves. Subtle but significant transcriptomic differences between upper and lower epidermal cells have been successfully distinguished. Furthermore, we discovered cell-type-specific gene expression gradients from the main vein to the leaf edge, which for the first time led to the finding of distinct spatial developmental trajectories of vascular cells and guard cells. Our study showcases the importance of physical locations of individual cells for exerting complex biologic functions in plants and demonstrates that scStereo-seq is a powerful tool to integrate single cell location and transcriptome information for plant biology study.

10Establishment of the pig testis spatial transcriptome atlasSource: STOmics DB (ID: STT0000068 )

Single-cell and spatial transcriptomics have revolutionized our understanding of cellular heterogeneity and gene expression patterns. In this study, we constructed the single-cell and spatial atlas of pig testis cells and identified the trajectory of germ cells and cell-cell communication to dissect the pig spermatogenesis process. Our findings shed new light on the molecular mechanisms underlying pig spermatogenesis and present a valuable resource for future studies investigating reproduction and breeding of pigs.