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quantitative whole transcriptome rna sequencing  (10X Genomics)

 
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    10X Genomics quantitative whole transcriptome rna sequencing
    Quantitative Whole Transcriptome Rna Sequencing, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/spatial+transcriptomics+sequencing+st+seq/visium/pmc10245699-26-16-20
    Average 86 stars, based on 1 article reviews
    quantitative whole transcriptome rna sequencing - by Bioz Stars, 2026-09
    86/100 stars

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    Related Articles

    Spatial Transcriptomics:

    Article Title: GenOT: generative optimal transport enables spatiotemporal interpolation and generation in cross-platform spatial transcriptomics.
    Article Snippet: .. The typical evolution of spatial transcriptomics technologies is characterized by continuous improvement in spatial resolution, ranging from 10x Genomics Visium (55 μm spot resolution, AR TIC LE IN PR ES S capturing approximately 1-10 cells per spot) [5], to Slide-seq (~10 μm, near-cellular resolution) [6], and finally to Stereo-seq (0.22 μm, subcellular resolution) [7]. ..

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    Article Title: GLP1-E2 therapy delays autoimmune diabetes in late-stage prediabetic NOD mice and potentiates low-dose anti-CD3 therapy for enhanced disease protection.
    Article Snippet: .. Analytically, we employed 10X Genomics Visium for spatial transcriptomics, which lacks true single-cell resolution compared with newer platforms such as Visium HD or Xenium. ..

    Article Title: Analysis of unmapped RNA-seq data from cancer spatial transcriptome toward characterizing cancer microbiome.
    Article Snippet: .. Recently, spatial transcriptomics, especially Visium (10X genomics, USA), has been garnering significant attention in cancer research. ..

    Fluorescence:

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    In Situ Hybridization:

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    Labeling:

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    Gene Expression:

    Article Title: Understanding nerve–tumor interactions: From basic biology to therapeutic innovation
    Article Snippet: .. 2D spatial transcriptomics, such as Visium (10x Genomics) and MERFISH (Multiplexed Error-Robust Fluorescence In Situ Hybridization), enable the precise mapping of transcriptomes to their corresponding locations in a 2D plane., , Compared with high-plex protein labeling, 2D spatial transcriptomics offers high-resolution spatial gene expression data and facilitates the discovery of novel spatially regulated genes within the TME. ..

    other:

    Article Title: Integrative single-cell and spatial multi-Omics analyses identify NETs-driven colon cancer subtypes with distinct metabolic features and prognostic implications.
    Article Snippet: ACC, Adrenocortical Carcinoma; ARRDC1, Arrestin Domain Containing 1; AUC, Area Under the Curve; AUCell, Area Under the Curve Cell-level scoring; BH, Benjamini–Hochberg; BLCA, Bladder Urothelial Carcinoma; AR TIC LE IN PR ES S BRCA, Breast Cancer; CESC, Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma; CHOL, Cholangiocarcinoma; CI, Confidence Interval; CNV, Copy Number Variation; COAD, Colon Adenocarcinoma; CRC, Colorectal Cancer; CSS, Cancer-Specific Survival; CXCR4, C-X-C Chemokine Receptor Type 4; DEGs, Differentially Expressed Genes; DUSP5, Dual-Specificity Phosphatase 5; ELISA, Enzyme-Linked Immunosorbent Assay; eQTL, Expression Quantitative Trait Locus; ESCA, Esophageal Carcinoma; FDR, False Discovery Rate; GDSC, Genomics of Drug Sensitivity in Cancer; GEO, Gene Expression Omnibus; GO, Gene Ontology; GSEA, Gene Set Enrichment Analysis; GWAS, Genome-Wide Association Study; HNSC, Head and Neck Squamous Cell Carcinoma; HPA, Human Protein Atlas; HR, Hazard Ratio; IC50, Half-Maximal Inhibitory Concentration; ICIs, Immune Checkpoint Inhibitors; KEGG, Kyoto Encyclopedia of Genes and Genomes; KICH, Kidney Chromophobe; KIRC, Kidney Renal Clear Cell Carcinoma; KM, Kaplan–Meier; AR TIC LE IN PR ES S LASSO, Least Absolute Shrinkage and Selection Operator; LGG, Low-Grade Glioma; LUAD, Lung Adenocarcinoma; MAPK, Mitogen-Activated Protein Kinase; MD, Molecular Dynamics; MESO, Mesothelioma; MIA, Multimodal Intersection Analysis; MIF, Macrophage Migration Inhibitory Factor; NETs, Neutrophil Extracellular Traps; OS, Overall Survival; PCA, Principal Component Analysis; READ, Rectal Adenocarcinoma; RMSD, Root Mean Square Deviation; ROC, Receiver Operating Characteristic; ROS, Reactive Oxygen Species; SARC, Sarcoma; scRNA-seq, Single-Cell RNA Sequencing; SLC2A3, Solute Carrier Family 2 Member 3; SNV, Single Nucleotide Variant; ssGSEA, Single-Sample Gene Set Enrichment Analysis; STAD, Stomach Adenocarcinoma; TAMs, Tumor-Associated Macrophages; TANs, Tumor-Associated Neutrophils; TCGA, The Cancer Genome Atlas; THCA, Thyroid Carcinoma; THYM, Thymoma; TIDE, Tumor Immune Dysfunction and Exclusion; TME, Tumor Microenvironment; TPM, Transcripts Per Million; AR TIC LE IN PR ES S Tregs, Regulatory T Cells; TUBB2A, Tubulin Beta Class 2A; UCEC, Uterine Corpus Endometrial Carcinoma; UMI, Unique Molecular Identifier; UVM, Uveal Melanoma; Visium, 10x Genomics Visium

    Single Cell:

    Article Title: GLP1-E2 therapy delays autoimmune diabetes in late-stage prediabetic NOD mice and potentiates low-dose anti-CD3 therapy for enhanced disease protection.
    Article Snippet: .. Analytically, we employed 10X Genomics Visium for spatial transcriptomics, which lacks true single-cell resolution compared with newer platforms such as Visium HD or Xenium. ..

    Expressing:

    Article Title: SpatialBench : Comparative cross-platform benchmarking of high-resolution spatial transcriptomics using matched mouse lymphoid tissue
    Article Snippet: .. The original Visium (10x Genomics) became the most widely adopted sST platform ( ) , offering transcriptome-wide coverage while aggregating expression from multiple cells per 55 μm resolution that aggregates expression from multiple cells per spot ( , ) . ..



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    Transcription programs of ccRCC cells in response to cuproptosis. A UMAP showing the 10 subtypes of 26,981 Epithelial cells; B heatmap showing inferred CNV of scRNA-seq dataset; C dot plot of the relative cellular proportions of Epithelial subtypes in each group; D GSEA analysis revealed the activated CRGs enriched in Normal Epithelial cells; E violin plot showing the relative CRGs score in each cancer subtype; F survival plot of HILPDA + ccRCC1 signature high and low group in the KIRC samples; G violin plots of HILPDA expression levels and hypoxia scores in each cancer subtypes; H spatial <t>transcriptome</t> displayed the distribution of CRGs, HILPDA + ccRCC1 signatures, hypoxia scores and HILPDA expression; I the regulon specificity scores of TFs in HILPDA + ccRCC1 subtype. The top 5 TFs ordered by scores were listed; J violin plot showing the expression levels of the top 5 TFs in HILPDA + ccRCC1 subtype across stage I–IV.
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    Transcription programs of ccRCC cells in response to cuproptosis. A UMAP showing the 10 subtypes of 26,981 Epithelial cells; B heatmap showing inferred CNV of scRNA-seq dataset; C dot plot of the relative cellular proportions of Epithelial subtypes in each group; D GSEA analysis revealed the activated CRGs enriched in Normal Epithelial cells; E violin plot showing the relative CRGs score in each cancer subtype; F survival plot of HILPDA + ccRCC1 signature high and low group in the KIRC samples; G violin plots of HILPDA expression levels and hypoxia scores in each cancer subtypes; H spatial <t>transcriptome</t> displayed the distribution of CRGs, HILPDA + ccRCC1 signatures, hypoxia scores and HILPDA expression; I the regulon specificity scores of TFs in HILPDA + ccRCC1 subtype. The top 5 TFs ordered by scores were listed; J violin plot showing the expression levels of the top 5 TFs in HILPDA + ccRCC1 subtype across stage I–IV.
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    Image Search Results


    Transcription programs of ccRCC cells in response to cuproptosis. A UMAP showing the 10 subtypes of 26,981 Epithelial cells; B heatmap showing inferred CNV of scRNA-seq dataset; C dot plot of the relative cellular proportions of Epithelial subtypes in each group; D GSEA analysis revealed the activated CRGs enriched in Normal Epithelial cells; E violin plot showing the relative CRGs score in each cancer subtype; F survival plot of HILPDA + ccRCC1 signature high and low group in the KIRC samples; G violin plots of HILPDA expression levels and hypoxia scores in each cancer subtypes; H spatial transcriptome displayed the distribution of CRGs, HILPDA + ccRCC1 signatures, hypoxia scores and HILPDA expression; I the regulon specificity scores of TFs in HILPDA + ccRCC1 subtype. The top 5 TFs ordered by scores were listed; J violin plot showing the expression levels of the top 5 TFs in HILPDA + ccRCC1 subtype across stage I–IV.

    Journal: Discover Oncology

    Article Title: Characterization of cuproptosis signature in clear cell renal cell carcinoma by single cell and spatial transcriptome analysis

    doi: 10.1007/s12672-024-01162-2

    Figure Lengend Snippet: Transcription programs of ccRCC cells in response to cuproptosis. A UMAP showing the 10 subtypes of 26,981 Epithelial cells; B heatmap showing inferred CNV of scRNA-seq dataset; C dot plot of the relative cellular proportions of Epithelial subtypes in each group; D GSEA analysis revealed the activated CRGs enriched in Normal Epithelial cells; E violin plot showing the relative CRGs score in each cancer subtype; F survival plot of HILPDA + ccRCC1 signature high and low group in the KIRC samples; G violin plots of HILPDA expression levels and hypoxia scores in each cancer subtypes; H spatial transcriptome displayed the distribution of CRGs, HILPDA + ccRCC1 signatures, hypoxia scores and HILPDA expression; I the regulon specificity scores of TFs in HILPDA + ccRCC1 subtype. The top 5 TFs ordered by scores were listed; J violin plot showing the expression levels of the top 5 TFs in HILPDA + ccRCC1 subtype across stage I–IV.

    Article Snippet: The spatial transcriptome sequencing (ST-seq) dataset was obtained from Mendeley Data platform ( https://data.mendeley.com/datasets/g67bkbnhhg/1 ) and input to python environment.

    Techniques: Expressing

    Dissection of immunosuppressive cells of cuproptosis-related tumor microenvironment. A UMAP showing the 16 subtypes of 99,210 Immune cells; B violin plot of the relative expression levels of the canocial markers in each subtype; C heatmap showing the enrichment of immune checkpoint and suppressive genes; D spatial transcriptome displayed the distribution of Treg, CD8_Exhausted and TAM signature scores; E heatmap showing the four gene expression patterns deduced by TDEseq analysis; F violin plots showing the relative expression levels of CRG scores in the immunosuppressive cells across different stages; G Chord diagram showing the number of interactions among the four subtypes; H Bubble plot showing the ligand-receptor pairs in the main subtype; I Heatmap showing the relative expression levels of key genes of the four subtypes among the different stages. The paired ligand-receptor shown in H were connected by lines.

    Journal: Discover Oncology

    Article Title: Characterization of cuproptosis signature in clear cell renal cell carcinoma by single cell and spatial transcriptome analysis

    doi: 10.1007/s12672-024-01162-2

    Figure Lengend Snippet: Dissection of immunosuppressive cells of cuproptosis-related tumor microenvironment. A UMAP showing the 16 subtypes of 99,210 Immune cells; B violin plot of the relative expression levels of the canocial markers in each subtype; C heatmap showing the enrichment of immune checkpoint and suppressive genes; D spatial transcriptome displayed the distribution of Treg, CD8_Exhausted and TAM signature scores; E heatmap showing the four gene expression patterns deduced by TDEseq analysis; F violin plots showing the relative expression levels of CRG scores in the immunosuppressive cells across different stages; G Chord diagram showing the number of interactions among the four subtypes; H Bubble plot showing the ligand-receptor pairs in the main subtype; I Heatmap showing the relative expression levels of key genes of the four subtypes among the different stages. The paired ligand-receptor shown in H were connected by lines.

    Article Snippet: The spatial transcriptome sequencing (ST-seq) dataset was obtained from Mendeley Data platform ( https://data.mendeley.com/datasets/g67bkbnhhg/1 ) and input to python environment.

    Techniques: Dissection, Expressing, Gene Expression