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stomics open  (Complete Genomics Inc)


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    Complete Genomics Inc stomics open
    Stomics Open, supplied by Complete Genomics Inc, used in various techniques. Bioz Stars score: 99/100, based on 485 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/stereo+seq+data/Stereo-seq+Transcriptomics+Set+for+FFPE/pm42107067-348-19-19
    Average 99 stars, based on 485 article reviews
    stomics open - by Bioz Stars, 2026-11
    99/100 stars

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    Related Articles

    other:

    Article Title: Spatiotemporal Transcriptomic Profiling Reveals the Dynamic Immunological Landscape of Alveolar Echinococcosis.
    Article Snippet: Preliminary Processing of Stereo-seq Data: The Stereo-seq raw data were automatically processed using the BGI STOmics analytical pipeline (https://cloud.stomics.tech/), including barcode demultiplexing, adapter filtering, mapping to reference genomes, deduplication, and quantification.

    Generated:

    Article Title: Spatial Flux Balance Analysis reveals tissue-of-origin and spatially dependent metabolic rewiring in renal and colorectal cancer
    Article Snippet: .. Stereo-seq data were generated as part of 2023 STOmics Grant 32, offered by BGI Genomics to D.M. ..

    Article Title: Spatial FBA reveals heterogeneous Warburg niches in renal tumors and lactate consumption in colorectal cancer.
    Article Snippet: .. Stereo-seq data were generated as part of 2023 STOmics Grant 32, offered by BGI Genomics to D.M. ..

    Olfactory:

    Article Title: MENDER: fast and scalable tissue structure identification in spatial omics data.
    Article Snippet: .. STARmap Prelimbic area data: [https://github.com/zhengli09/BASS-Analysis/ tree/master/data]; BaristaSeq Visual cortex data: [https://spacetx. github.io/data.html]; MERFISH Frontal cortex data: [https:// cellxgene.cziscience.com/collections/ 31937775-0602-4e52-a799b6acdd2bac2e]; MERSCOPE (Vizgen) Brain data: [https://info.vizgen. com/mouse-brain-data]; ST Olfactory bulb data: [https://www. spatialresearch.org/resources-published-datasets/]; Visium data: [https://www.10xgenomics.com/resources/datasets]; Slide-seq data: [https://singlecell.broadinstitute.org/single_cell/study/SCP815/ sensitive-spatial-genome-wide-expression-profiling-at-cellularresolution#study-summary]; Stereo-Seq data: [https://db.cngb.org/ stomics/datasets/STDS0000058]; osmFISH data: [http:// linnarssonlab.org/osmFISH/]; ExSeq data: [10.5281/zenodo.4075515]; STARmapPLUS data: [https://singlecell.broadinstitute.org/single_cell/ study/SCP1375]; Allen Reference Atlas: [https://mouse.brain-map.org/ experiment/thumbnails/100048576?image_type=atlas]; We also provide the benchmark datasets as h5ad format via SODB31, please find how to load them in the tutorial [https://mender-tutorial.readthedocs. io/en/latest/]. ..



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    Single-nucleus transcriptome and spatial <t>transcriptomics</t> landscape of the ileal tissue of SAP and CON group rats. (A) Schematic illustration of the workflow for this study. (B) Representative Hematoxylin and Eosin (H&E)–stained ileal sections from CON and SAP rats. (C) UMAP plot of single-nucleus transcriptome profiles of SAP and CON group samples. Colors indicate groups, clusters and cell types. (D) Heatmap plot of marker genes for cell annotation. (E) Bar plot showing cell-type proportions (mean ± SEM) in snRNA-seq data. (F) Spatial transcriptomics profiles of SAP and CON group samples. Colors indicate cell types. (G) Bar plot showing cell-type proportions (mean ± SEM) in spatial transcriptomics (Stereo-seq) data. Statistical significance: ns, not significant; *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.
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    Image Search Results


    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.

    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

    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

    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:

    Single-nucleus transcriptome and spatial transcriptomics landscape of the ileal tissue of SAP and CON group rats. (A) Schematic illustration of the workflow for this study. (B) Representative Hematoxylin and Eosin (H&E)–stained ileal sections from CON and SAP rats. (C) UMAP plot of single-nucleus transcriptome profiles of SAP and CON group samples. Colors indicate groups, clusters and cell types. (D) Heatmap plot of marker genes for cell annotation. (E) Bar plot showing cell-type proportions (mean ± SEM) in snRNA-seq data. (F) Spatial transcriptomics profiles of SAP and CON group samples. Colors indicate cell types. (G) Bar plot showing cell-type proportions (mean ± SEM) in spatial transcriptomics (Stereo-seq) data. Statistical significance: ns, not significant; *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.

    Journal: Frontiers in Immunology

    Article Title: Single-nucleus and spatial transcriptomics reveal intestinal cellular heterogeneity, differentiation, and cell communication mechanisms in SAP-induced intestinal injury

    doi: 10.3389/fimmu.2026.1719902

    Figure Lengend Snippet: Single-nucleus transcriptome and spatial transcriptomics landscape of the ileal tissue of SAP and CON group rats. (A) Schematic illustration of the workflow for this study. (B) Representative Hematoxylin and Eosin (H&E)–stained ileal sections from CON and SAP rats. (C) UMAP plot of single-nucleus transcriptome profiles of SAP and CON group samples. Colors indicate groups, clusters and cell types. (D) Heatmap plot of marker genes for cell annotation. (E) Bar plot showing cell-type proportions (mean ± SEM) in snRNA-seq data. (F) Spatial transcriptomics profiles of SAP and CON group samples. Colors indicate cell types. (G) Bar plot showing cell-type proportions (mean ± SEM) in spatial transcriptomics (Stereo-seq) data. Statistical significance: ns, not significant; *P < 0.05; **P < 0.01; ***P < 0.001; ****P < 0.0001.

    Article Snippet: The spatial transcriptomics data were obtained according to the protocol of STOmics Gene Expression Set-S1 on the website ( https://www.stomics.tech/ ), which is an improved version of initial procedures.

    Techniques: Spatial Transcriptomics, Staining, Marker