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spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform  (10X Genomics)

 
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    10X Genomics spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform
    Spatial Transcriptome Rna Sequencing (Strna Seq) Data For Breast Cancer Samples, Specific To The 10x Visium Platform, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/visium+spatial+transcriptomics+sequencing+data/cells+generated+with+the+10x+genomics+3%E2%80%99+v+2+protocol/pm38450906-83-9-20
    Average 90 stars, based on 1 article reviews
    spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    RNA Sequencing:

    Article Title: A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data
    Article Snippet: .. We downloaded RNA-seq bam files of the 10X Visium data of a fresh frozen adult mouse coronal brain section sample from https://www.10xgenomics.com/datasets/adult-mouse-brain-coronal-section-fresh-frozen-1-standard , and the Slide-seqV2 data of adult mouse hippocampus from https://singlecell.broadinstitute.org/single_cell/study/SCP815/sensitive-spatial-genome-wide-expression-profiling-at-cellular-resolution#study-summary . ..

    other:

    Article Title: CPARI: a novel approach combining cell partitioning with absolute and relative imputation to address dropout in single-cell RNA-seq data.
    Article Snippet: Summary of the simulated scRNA-seq datasets Dataset name Cell type Subtype number Gene number Cell number Sequencing platform PBMC [29] Peripheral blood mononuclear cells 8 16449 4271 10X Genomics Worm neuron cells [30] Worm neuronal cells 10 13488 4186 Sci-RNA-seq Mouse bladder cells [31] Mouse bladder cells 16 20670 2746 Microwell-seq LPS [32] Various cells 4 2047 306 Array Figure 2.

    Expressing:

    Article Title: Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
    Article Snippet: .. 8 ● Differential transcript usage, differential transcript expression and differential gene expression analysis ○ For the cell line gene expression analysis, in addition to good library-level correlation of gene quantitation between targeted short- and long-read methods (Supplementary Fig. 4), we observe good concordance in DEGs among matched individual cell lines across both methods: ○ The 10x Genomics gene expression kit is significantly biased towards the 3’ end of transcripts (see response to comment 4, which shows short-read metagene coverage). ..

    Gene Expression:

    Article Title: Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
    Article Snippet: .. 8 ● Differential transcript usage, differential transcript expression and differential gene expression analysis ○ For the cell line gene expression analysis, in addition to good library-level correlation of gene quantitation between targeted short- and long-read methods (Supplementary Fig. 4), we observe good concordance in DEGs among matched individual cell lines across both methods: ○ The 10x Genomics gene expression kit is significantly biased towards the 3’ end of transcripts (see response to comment 4, which shows short-read metagene coverage). ..

    Article Title: Benchmarking computational methods for single-cell chromatin data analysis
    Article Snippet: .. For the unprocessed data, fragment files of the cell line dataset were downloaded from GEO accession GSE162690 [ ], fragment file and the gene expression matrix file of the 10X PBMC multiomics dataset were downloaded from https://www.10xgenomics.com/resources/datasets/pbmc-from-a-healthy-donor-granulocytes-removed-through-cell-sorting-10-k-1-standard-1-0-0 , and fragment files of the human adult atlas datasets were downloaded from GEO accession GSE184462 [ ]. ..

    Quantitation Assay:

    Article Title: Single-cell long-read targeted sequencing reveals transcriptional variation in ovarian cancer
    Article Snippet: .. 8 ● Differential transcript usage, differential transcript expression and differential gene expression analysis ○ For the cell line gene expression analysis, in addition to good library-level correlation of gene quantitation between targeted short- and long-read methods (Supplementary Fig. 4), we observe good concordance in DEGs among matched individual cell lines across both methods: ○ The 10x Genomics gene expression kit is significantly biased towards the 3’ end of transcripts (see response to comment 4, which shows short-read metagene coverage). ..

    Formalin-fixed Paraffin-Embedded:

    Article Title: Spatial transcriptomic analysis drives PET imaging of tight junction protein expression in pancreatic cancer theranostics
    Article Snippet: .. Formalin-fixed, paraffin-embedded (FFPE) human pancreatic cancer tissue sections were placed on spatial transcriptomic slides for spatial transcriptomic sequencing based on the 10x FFPE workflow (10x Genomics, Pleasanton, CA). .. Individually indexed libraries were sequenced on the Novaseq 6000 (Illumina Inc., San Diego, CA).

    Sequencing:

    Article Title: Spatial transcriptomic analysis drives PET imaging of tight junction protein expression in pancreatic cancer theranostics
    Article Snippet: .. Formalin-fixed, paraffin-embedded (FFPE) human pancreatic cancer tissue sections were placed on spatial transcriptomic slides for spatial transcriptomic sequencing based on the 10x FFPE workflow (10x Genomics, Pleasanton, CA). .. Individually indexed libraries were sequenced on the Novaseq 6000 (Illumina Inc., San Diego, CA).



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    Spatial <t>Transcriptomics</t> in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA <t>sequencing</t> with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.
    Visium Spatial Transcriptomics Sequencing Data, supplied by Spatial Transcriptomics Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform  (10X Genomics)
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    10X Genomics spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform
    Spatial <t>Transcriptomics</t> in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA <t>sequencing</t> with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.
    Spatial Transcriptome Rna Sequencing (Strna Seq) Data For Breast Cancer Samples, Specific To The 10x Visium Platform, supplied by 10X Genomics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/visium+spatial+transcriptomics+sequencing+data/cells+generated+with+the+10x+genomics+3%E2%80%99+v+2+protocol/pm38450906-83-9-20
    Average 90 stars, based on 1 article reviews
    spatial transcriptome rna sequencing (strna-seq) data for breast cancer samples, specific to the 10x visium platform - by Bioz Stars, 2026-11
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    Spatial Transcriptomics in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA sequencing with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.

    Journal: iScience

    Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

    doi: 10.1016/j.isci.2024.110018

    Figure Lengend Snippet: Spatial Transcriptomics in horizontally sectioned E14.5 mouse diaphragm identifies distinct tissues and muscle domains (A) Schematic representation of embryonic mouse diaphragm in which relevant anatomical regions are indicated. NMJ: Neuromuscular junction, MTJ: Myotendinous junction. (B) SpatialFeaturePlots demonstrating expression levels and distributions of representative genes for muscle, NMJ, MTJ and tendon. (C) SpatialDimPlot demonstrating the distribution of all the identified clusters within the diaphragm tissue. (D) Spatial distribution of representative Seurat clusters differentiating genetically specific domains in developing mouse diaphragm. (E) Uniform Manifold Approximation and Projection (UMAP) diagram of identified clusters of spatial RNA sequencing with muscle and endothelial clusters at the left and tendon and erythrocyte clusters at right. (F) FeaturePlots showing expression of muscle ( Ttn , Myh3 , Myh8 ), crural diaphragm ( Crlf1 ), NMJ ( Chrna1 , Chrng , Musk, Etv5 ), MTJ ( Col22a1 , Ankrd1 , Rxrg , Csrp3 ) and tendon ( Col12a1 , Antxr1, Tnmd , Tnc ) markers displayed by UMAP.

    Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

    Techniques: Expressing, RNA Sequencing

    Spatial Transcriptomics reveals distinct myogenic processes in the muscle center and periphery in E14.5 mouse diaphragm (A) SpatialFeaturePlots demonstrating expression levels and distributions of myogenic differentiation markers. (B) VlnPlots of expression levels of genes in clusters identified as muscle center, default muscle, and muscle periphery show an overall increase or decrease in expression of genes involved in muscle development from the center to the periphery. Y axis indicates expression levels. (C) Cnetplots showing GO terms in biological processes (red nodes) and their associated genes (blue nodes) for the upregulated genes in clusters annotated as muscle center compared to muscle periphery (top) or muscle periphery compared to muscle center (bottom). (D) Dotplots of expression of genes involved in myogenesis displaying a declining (right) or increasing (left) gradient in clusters from the muscle center, over default muscle (muscle middle), to the muscle periphery.

    Journal: iScience

    Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

    doi: 10.1016/j.isci.2024.110018

    Figure Lengend Snippet: Spatial Transcriptomics reveals distinct myogenic processes in the muscle center and periphery in E14.5 mouse diaphragm (A) SpatialFeaturePlots demonstrating expression levels and distributions of myogenic differentiation markers. (B) VlnPlots of expression levels of genes in clusters identified as muscle center, default muscle, and muscle periphery show an overall increase or decrease in expression of genes involved in muscle development from the center to the periphery. Y axis indicates expression levels. (C) Cnetplots showing GO terms in biological processes (red nodes) and their associated genes (blue nodes) for the upregulated genes in clusters annotated as muscle center compared to muscle periphery (top) or muscle periphery compared to muscle center (bottom). (D) Dotplots of expression of genes involved in myogenesis displaying a declining (right) or increasing (left) gradient in clusters from the muscle center, over default muscle (muscle middle), to the muscle periphery.

    Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

    Techniques: Expressing

    Spatial Transcriptomics in horizontally sectioned E18.5 mouse diaphragm identifies specific functional muscle domains and fiber types (A) SpatialFeaturePlots demonstrating expression levels and distributions of NMJ genes ( Chrna1 , Musk , Etv5 , Ache , Chrng, Chrne ), neonatal ( Myh8 ) and embryonic ( Myh3 ) myosin heavy chains, developmental troponin Tnnt2 , and ventral diaphragm markers ( Myog , Flnc , Csrp3 ). (B) Spatial distribution of Seurat clusters of distinct muscle and tendon domains. (C) UMAP representation of identified clusters of spatial RNA sequencing indicates spatially and functionally divergent differentiation of diaphragm muscle. (D) FeaturePlots demonstrating expression of muscle ( Ttn , Myh3 , Myh8 ), type I muscle ( Myh7, Myl2, Myl3 ), type IIb muscle ( Myh4 , Pvalb , Mybpc2 ), NMJ ( Chrna1 , Musk , Etv5 ), MTJ ( Col22a1 , Ankrd1 , Uchl1 ) and tendon ( Tnmd , Col11a1 , Scx ) markers displayed by UMAP.

    Journal: iScience

    Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

    doi: 10.1016/j.isci.2024.110018

    Figure Lengend Snippet: Spatial Transcriptomics in horizontally sectioned E18.5 mouse diaphragm identifies specific functional muscle domains and fiber types (A) SpatialFeaturePlots demonstrating expression levels and distributions of NMJ genes ( Chrna1 , Musk , Etv5 , Ache , Chrng, Chrne ), neonatal ( Myh8 ) and embryonic ( Myh3 ) myosin heavy chains, developmental troponin Tnnt2 , and ventral diaphragm markers ( Myog , Flnc , Csrp3 ). (B) Spatial distribution of Seurat clusters of distinct muscle and tendon domains. (C) UMAP representation of identified clusters of spatial RNA sequencing indicates spatially and functionally divergent differentiation of diaphragm muscle. (D) FeaturePlots demonstrating expression of muscle ( Ttn , Myh3 , Myh8 ), type I muscle ( Myh7, Myl2, Myl3 ), type IIb muscle ( Myh4 , Pvalb , Mybpc2 ), NMJ ( Chrna1 , Musk , Etv5 ), MTJ ( Col22a1 , Ankrd1 , Uchl1 ) and tendon ( Tnmd , Col11a1 , Scx ) markers displayed by UMAP.

    Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

    Techniques: Functional Assay, Expressing, RNA Sequencing

    Spatial transcriptomics reveals aberrant regulation of myogenic genes in Ca V 1.1 −/− mice (A) FeaturePlots showing expression of Ttn (muscle), Chrna1 and Musk (NMJ) displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (B) Violin plots showing expression of representative genes differentially expressed in control and Ca V 1.1 −/− samples at E14.5 and E18.5. Y axis indicates expression level. (C) FeaturePlots of module scores of muscle differentiation markers displayed by UMAP in E18.5 control and Ca V 1.1 −/− integrated dataset show increased expression of early markers (top) and a decreased expression of late markers (bottom) in Ca V 1.1 −/− muscles. (D) Venn diagrams of top 200 DEGs genes and GO terms for these genes between E14.5 control and E18.5 control and between E18.5 Ca V 1.1 −/− and E18.5 control muscles indicate more shared genes and GO terms for upregulated genes in E18.5 Ca V 1.1 −/− with E14.5 control muscle and for downregulated genes in E18.5 Ca V 1.1 −/− with E18.5 control muscle. (E) FeaturePlots showing expression of Klf5 and Tead4 displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (F) Violin plots of Klf5 and Tead4 expression in muscle clusters of E14.5 and E18.5 control and Ca V 1.1 −/− spatial datasets. Y axis indicates expression level.

    Journal: iScience

    Article Title: Spatial transcriptomics in embryonic mouse diaphragm muscle reveals regional gradients and subdomains of developmental gene expression

    doi: 10.1016/j.isci.2024.110018

    Figure Lengend Snippet: Spatial transcriptomics reveals aberrant regulation of myogenic genes in Ca V 1.1 −/− mice (A) FeaturePlots showing expression of Ttn (muscle), Chrna1 and Musk (NMJ) displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (B) Violin plots showing expression of representative genes differentially expressed in control and Ca V 1.1 −/− samples at E14.5 and E18.5. Y axis indicates expression level. (C) FeaturePlots of module scores of muscle differentiation markers displayed by UMAP in E18.5 control and Ca V 1.1 −/− integrated dataset show increased expression of early markers (top) and a decreased expression of late markers (bottom) in Ca V 1.1 −/− muscles. (D) Venn diagrams of top 200 DEGs genes and GO terms for these genes between E14.5 control and E18.5 control and between E18.5 Ca V 1.1 −/− and E18.5 control muscles indicate more shared genes and GO terms for upregulated genes in E18.5 Ca V 1.1 −/− with E14.5 control muscle and for downregulated genes in E18.5 Ca V 1.1 −/− with E18.5 control muscle. (E) FeaturePlots showing expression of Klf5 and Tead4 displayed by UMAP in control and Ca V 1.1 −/− integrated dataset at E14.5 (left) and E18.5 (right). (F) Violin plots of Klf5 and Tead4 expression in muscle clusters of E14.5 and E18.5 control and Ca V 1.1 −/− spatial datasets. Y axis indicates expression level.

    Article Snippet: Visium Spatial Transcriptomics sequencing data were aligned using the default SpaceRanger (2.0.1) pipeline for FFPE slides in a Singularity Container running Ubuntu 22.04 on a high-performance cluster (Medical University of Innsbruck).

    Techniques: Expressing, Control, Muscles