Journal: bioRxiv

Article Title: Single-cell transcriptomic atlas of mouse oocyte development from growth to ovulation

doi: 10.64898/2026.03.11.710939

Figure Lengend Snippet: a , UMAP of GCs, colored by seven GC subtypes (Progenitor, Preantral 1, Preantral 2, Mitotic 1, Mitotic 2, Antral Mural and Atretic). b , Feature plots of representative subtype markers on the UMAP. c , Monocle3 pseudotime trajectory inferred for GCs, with the principal graph overlaid and direction indicated from progenitor toward antral mural cells. d , Heatmap of representative genes showing coordinated expression changes along the progenitor-to-mural trajectory (expression shown as z-scores). e , Heatmap of Hallmark ssGSEA scores across granulosa subtypes (z-scored per gene set). f , H&E image of a Stereo-seq FF V1.3 mouse ovary section (6-8 weeks old), with representative regions (α–θ) indicated. Scale bar, 100 μm. g , Cell2location-based spatial mapping of GC subtypes at cell-bin resolution. h , Zoom-in views of representative regions (α, β, γ, and θ) showing H&E morphology and spatial expression of selected marker genes. Scale bar, 50 μm.

Article Snippet: Publicly available mouse ovary Stereo-seq Transcriptomics FF v1.3 demo data were obtained from the STOmics website ( https://www.stomics.tech/col1347 ).

Techniques: Expressing, Marker

Journal: bioRxiv

Article Title: Single-cell transcriptomic atlas of mouse oocyte development from growth to ovulation

doi: 10.64898/2026.03.11.710939

Figure Lengend Snippet: Spatial maps showing cell2location-predicted localization of each annotated cell subtype on the Stereo-seq FF V1.3 ovary section (6–8 weeks old), displayed separately by subtype. Scale bar, 100 μm

Article Snippet: Publicly available mouse ovary Stereo-seq Transcriptomics FF v1.3 demo data were obtained from the STOmics website ( https://www.stomics.tech/col1347 ).

Techniques:

Journal: Frontiers in Immunology

Article Title: Decoding the spatial logic of immune evasion in hepatocellular carcinoma: from single-cell profiling to spatial omics

doi: 10.3389/fimmu.2026.1935648

Figure Lengend Snippet: Comprehensive comparison of scRNA-seq and spatial omics technologies in oncology.

Article Snippet: Sequencing-based spatial transcriptomics , Visium (10x Genomics); Stereo-seq (BGI); Slide-seq , Whole-transcriptome mapping across large tissue areas; resolution ranges from multi-cellular spots to subcellular/nanoscale platforms. , Maps tissue-scale architecture, spatial gene modules, subclonal competition zones and tumor-stroma boundaries. , Resolution-sensitivity trade-off; multi-cellular spots require deconvolution; high sequencing cost..

Techniques: Comparison, Single Cell, Profiling, Sample Throughput, Sequencing, Spatial Transcriptomics, Tissue, Imaging, Sampling, In Situ, Transcriptomics, Functional Assay, Multiplexing, Biomarker Discovery

Journal: GigaScience

Article Title: StereoSiTE: a framework to spatially and quantitatively profile the cellular neighborhood organized iTME

doi: 10.1093/gigascience/giae078

Figure Lengend Snippet: Spatial transcriptomic mapping of xenograft model in situ . (A) Flowchart illustrating the construction of the xenograft model is presented. BALB/c mice were subcutaneously injected with CT26 cells derived from colon cancer. Subsequently, the mice were either treated with a vehicle or DMXAA for a period of 14 days posttumor transplantation. Tissue samples were collected 24 hours after the treatment. (B) Heatmap depicting the expression of transcriptional markers of 11 annotated immune cell types at a single-cell resolution is shown. (C) An analysis of the proportion of immune cells at a single-cell resolution in each sample is provided. (D) Histogram comparing nonimmune cells to immune cells is displayed, where the blue bar represents the proportion of nonimmune cells, and the gray bar represents the integrated proportion of immune cells. The numbers associated with each bar indicate the precise cell counts for each sample. (E) Representative hematoxylin and eosin staining images of sample 717 from the control group (left) and sample 718 from the treatment group (right) are presented. The red-thread restricted region highlights the necrotic site. (F) In situ visualization of annotated cell types using stereo-seq data is shown on the left, an enlarged image of the marked-circle-site displaying cellular compositions is in the middle, and representative immunohistochemistry staining (CD163 indicating macrophages in sample 717 and Ly6G indicating neutrophils in sample 718) of the same marked-circle-site is presented on the right.

Article Snippet: The prepared section underwent processing in accordance with the Stereo-seq Transcriptomics Set User Manual (STOmics), utilizing reagents from the Stereo-seq Transcriptomics T kit and Stereo-seq Library Preparation kit (STOmics).

Techniques: In Situ, Injection, Derivative Assay, Transplantation Assay, Expressing, Staining, Control, Immunohistochemistry