1Single-cell and spatially resolved transcriptomic data of mouse regenerative livers under normal and fibrotic conditionsSource: STOmics DB (ID: STT0000057 )

A single-cell spatial-temporal transcriptomic atlas of liver regeneration under normal and fibrotic condition, including a total of 30 mouse liver samples obtained from 15 normal and 15 fibrotic mice at timepoints Day 0, 1, 2, 3, and 7 after a partial hepatectomy (PHx) procedure with three replicates for each time point, followed by the scRNA-seq and SRT sequencing for each sample using the Stereo-seq platform.

2human endometriumSource: STOmics DB (ID: STT0000132 )

scRNA-seq anda spatial transcriptomics

3stTransfer: Transfer single-cell annotation to spatial transcriptomics with single-cell resolutionSource: STOmics DB (ID: STT0000130 )

Spatial transcriptomics (ST) offers the opportunity to study gene expression patterns and the spatial microenvironment in situ. However, current ST sequencing technologies are often limited by low detection sensitivity and restricted gene throughput. Achieving precise cell type annotations for each cell within spatial transcriptomic data, which is essential for understanding biological processes at the single-cell level, remains a significant challenge. In this work, we present stTransfer, a novel method for annotating single cells in spatial transcriptomic data that integrates graph neural networks and transfer learning. This approach leverages existing information from reference single-cell RNA sequencing (scRNA-seq) datasets as well as the spatial context provided by spatial transcriptomics. Through a series of benchmark analyses on publicly available spatial transcriptomic datasets, we demonstrate that stTransfer outperforms other state-of-the-art methods in terms of accuracy and robustness. Furthermore, we applied stTransfer to a self-collected dataset of the zebra finch optic tectum, obtained using Stereo-seq technology. Our analysis led to the discovery of a distinct class of neurons, highlighting the potential of our method to uncover new insights into cellular diversity and organization.

4Single-cell and spatial transcriptomics reveal the immune microenvironment signaling regulatory network of NKTCLSource: STOmics DB (ID: STT0000114 )

This study aims to collect single-cell transcriptomic and spatial transcriptomic sequencing data from fresh NKTCL tissues, as well as perform whole exome sequencing on paraffin-embedded and peripheral blood samples, to delineate the tumor clonal subpopulations and tumor microenvironment heterogeneity in NKTCL patients.

5Spatiotemporal Transcriptome of the Developing to Mature Murine Hearts PostnatalSource: STOmics DB (ID: STT0000090 )

The processes governing the formation and maturation of the mammalian heart are still not fully understood. Specifically, crucial details regarding the diverse cell types involved in chamber formation during mammalian heart development remain elusive. In this study, we employed cutting-edge spatially resolved transcriptomic technology, Stereo-seq, and nucleus imputation technology to create an extensive dataset.

6test10x-sts0000006Source: STOmics DB (ID: STT0000002 )

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7stereo-seq of the cochlear nucleusSource: STOmics DB (ID: STT0000046 )

The molecular mechanisms underlying the complex functions of the cochlear nucleus (CN) remain poorly understood, requiring a thorough characterization of cellular properties. We utilized single-nuclei RNA sequencing (snRNA-seq) and spatial enhanced resolution omics-sequencing (Stereo-seq) to generate a comprehensive celluar and molecular atlas of the CN and further defined various cell types and functionally spatial regions. Meanwhile, we identified the marker genes for the neurons and regions that were not previously reported. We further investigated the spatial distribution of different cell types and found that the neurons exhibited considerable regional specialization, which may account for the functional region formation. Transcriptome comparisons between normal and congenital hearing loss animal models indicated that bushy cell is the major cell type exhibiting transcriptomic response to auditory stimuli, and the expression pattern and dynamics of Spp1 were highlighted in the comparison, and similar pattern was also observed during CN development with the establishment of hearing. We functionally confirmed that Spp1 is required to maintain normal auditory processing by formatting the high conduction velocities axons from Spp1-/- mice. Taken together, our study provides an integrative spatially resolved cellular map of the CN and identifies critical cell types and genes involved in hearing loss and its treatment.

8Spatiotemporal 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

9comprehensive 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.

10Public Datasets of STOmicsSource: STOmics DB (ID: STT0000124 )

Browse and obtain STOmics public datasets for further exploration needs.