Review



10x visium srt data  (10X Genomics)

 
  • Logo
  • About
  • News
  • Press Release
  • Team
  • Advisors
  • Partners
  • Contact
  • Bioz Stars
  • Bioz vStars
    • 86
      Buy from Supplier

    Structured Review

    10X Genomics 10x visium srt data
    10x Visium Srt Data, 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/visium+srt+data/cellranger/pm39127046-670-20-30
    Average 86 stars, based on 1 article reviews
    10x visium srt data - by Bioz Stars, 2026-09
    86/100 stars

    Images

    Related Articles

    Software:

    Article Title: Precise detection of cell-type-specific domains in spatial transcriptomics
    Article Snippet: The mouse brainscRNA-seq data from Zeisel et al. have been deposited at GEO: GSE60361 , and its annotated data have been deposited at http://linnarssonlab.org/cortex ; Visium SRT data are available at 10x Visium official websites ( https://www.10xgenomics.com/resources/datasets/mouse-brain-section-coronal-1-standard-1-0-0 ; https://www.10xgenomics.com/resources/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0 ).



    Similar Products

    10x visium srt data  (10X Genomics)
    86
    10X Genomics 10x visium srt data
    10x Visium Srt Data, 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/visium+srt+data/cellranger/pm39127046-670-20-30
    Average 86 stars, based on 1 article reviews
    10x visium srt data - by Bioz Stars, 2026-09
    86/100 stars
    		  Buy from Supplier
    visium srt data  (10X Genomics)
    90
    10X Genomics visium srt data

    Visium Srt Data, 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+srt+data/visium+srt+data/pmc11384096-336-25-36
    Average 90 stars, based on 1 article reviews
    visium srt data - by Bioz Stars, 2026-09
    90/100 stars
    		  Buy from Supplier
    srt data 10x genomics visium platform  (10X Genomics)
    90
    10X Genomics srt data 10x genomics visium platform
    We applied nnSVG , a method to identify spatially variable genes (SVGs), in the <t>Visium</t> <t>SRT</t> samples. We ran nnSVG within each contiguous tissue area containing a manually annotated LC region (13 tissue areas in the N =8 Visium samples) and calculated an overall ranking of top SVGs by averaging the ranks per gene from each tissue area. (A) The top 50 ranked SVGs from this analysis included a subset (11 out of 50) of genes that were highly ranked in samples from only one donor (Br8079, genes highlighted in maroon). We determined that this was due to the inclusion of a section of the choroid plexus adjacent to the LC for this donor. Bars show the number of times (out of 13 tissue areas) each gene was included within the top 100 SVGs. Rows are ordered by overall average ranking in descending order. (B) Spatial expression of CAPS , a choroid plexus marker gene, in the N =8 Visium samples. (C) Histology image showing the two tissue areas for sample Br8079_LC_round3. (D) In order to focus on LC-associated SVGs, we calculated an overall average ranking of SVGs that were each included within the top 100 SVGs in at least 10 out of the 13 tissue areas, which identified 32 highly-ranked, replicated LC-associated SVGs. Boxplots show the ranks in each tissue area. Rows are ordered by the overall average ranking in descending order.
    Srt Data 10x Genomics 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+srt+data/10x+genomics+visium/bio_rxiv__2022__10__28__514241-145-7-5
    Average 90 stars, based on 1 article reviews
    srt data 10x genomics visium platform - by Bioz Stars, 2026-09
    90/100 stars
    		  Buy from Supplier

    Image Search Results


    Journal: Cell Reports Methods

    Article Title: Precise detection of cell-type-specific domains in spatial transcriptomics

    doi: 10.1016/j.crmeth.2024.100841

    Figure Lengend Snippet:

    Article Snippet: The mouse brainscRNA-seq data from Zeisel et al. have been deposited at GEO: GSE60361 , and its annotated data have been deposited at http://linnarssonlab.org/cortex ; Visium SRT data are available at 10x Visium official websites ( https://www.10xgenomics.com/resources/datasets/mouse-brain-section-coronal-1-standard-1-0-0 ; https://www.10xgenomics.com/resources/datasets/adult-mouse-brain-ffpe-1-standard-1-3-0 ).

    Techniques: Software

    We applied nnSVG , a method to identify spatially variable genes (SVGs), in the Visium SRT samples. We ran nnSVG within each contiguous tissue area containing a manually annotated LC region (13 tissue areas in the N =8 Visium samples) and calculated an overall ranking of top SVGs by averaging the ranks per gene from each tissue area. (A) The top 50 ranked SVGs from this analysis included a subset (11 out of 50) of genes that were highly ranked in samples from only one donor (Br8079, genes highlighted in maroon). We determined that this was due to the inclusion of a section of the choroid plexus adjacent to the LC for this donor. Bars show the number of times (out of 13 tissue areas) each gene was included within the top 100 SVGs. Rows are ordered by overall average ranking in descending order. (B) Spatial expression of CAPS , a choroid plexus marker gene, in the N =8 Visium samples. (C) Histology image showing the two tissue areas for sample Br8079_LC_round3. (D) In order to focus on LC-associated SVGs, we calculated an overall average ranking of SVGs that were each included within the top 100 SVGs in at least 10 out of the 13 tissue areas, which identified 32 highly-ranked, replicated LC-associated SVGs. Boxplots show the ranks in each tissue area. Rows are ordered by the overall average ranking in descending order.

    Journal: bioRxiv

    Article Title: The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    doi: 10.1101/2022.10.28.514241

    Figure Lengend Snippet: We applied nnSVG , a method to identify spatially variable genes (SVGs), in the Visium SRT samples. We ran nnSVG within each contiguous tissue area containing a manually annotated LC region (13 tissue areas in the N =8 Visium samples) and calculated an overall ranking of top SVGs by averaging the ranks per gene from each tissue area. (A) The top 50 ranked SVGs from this analysis included a subset (11 out of 50) of genes that were highly ranked in samples from only one donor (Br8079, genes highlighted in maroon). We determined that this was due to the inclusion of a section of the choroid plexus adjacent to the LC for this donor. Bars show the number of times (out of 13 tissue areas) each gene was included within the top 100 SVGs. Rows are ordered by overall average ranking in descending order. (B) Spatial expression of CAPS , a choroid plexus marker gene, in the N =8 Visium samples. (C) Histology image showing the two tissue areas for sample Br8079_LC_round3. (D) In order to focus on LC-associated SVGs, we calculated an overall average ranking of SVGs that were each included within the top 100 SVGs in at least 10 out of the 13 tissue areas, which identified 32 highly-ranked, replicated LC-associated SVGs. Boxplots show the ranks in each tissue area. Rows are ordered by the overall average ranking in descending order.

    Article Snippet: The SRT data using the 10x Genomics Visium platform captures around 1-10 cells per measurement location in the human brain, and future studies could apply a higher-resolution platform to characterize expression at single-cell or sub-cellular spatial resolution.

    Techniques: Expressing, Marker

    (A-B) We visualized the spatial expression of 5-HT (5-hydroxytryptamine or serotonin) neuron marker genes ( TPH2 and SLC6A4 ) in the N =9 initial Visium SRT samples within the Visium SRT samples, which showed that the population of 5-HT neurons was distributed across both the LC and non-LC regions. (C) Enrichment of 5-HT neuron marker gene expression ( TPH2 and SLC6A4 ) within manually annotated LC regions compared to non-LC regions in the N =8 Visium SRT samples. Boxplots show values as mean log-transformed normalized counts (logcounts) per spot within each region per sample, with samples represented by shapes.

    Journal: bioRxiv

    Article Title: The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    doi: 10.1101/2022.10.28.514241

    Figure Lengend Snippet: (A-B) We visualized the spatial expression of 5-HT (5-hydroxytryptamine or serotonin) neuron marker genes ( TPH2 and SLC6A4 ) in the N =9 initial Visium SRT samples within the Visium SRT samples, which showed that the population of 5-HT neurons was distributed across both the LC and non-LC regions. (C) Enrichment of 5-HT neuron marker gene expression ( TPH2 and SLC6A4 ) within manually annotated LC regions compared to non-LC regions in the N =8 Visium SRT samples. Boxplots show values as mean log-transformed normalized counts (logcounts) per spot within each region per sample, with samples represented by shapes.

    Article Snippet: The SRT data using the 10x Genomics Visium platform captures around 1-10 cells per measurement location in the human brain, and future studies could apply a higher-resolution platform to characterize expression at single-cell or sub-cellular spatial resolution.

    Techniques: Expressing, Marker, Transformation Assay

    We applied a spot-level deconvolution algorithm (cell2location ) to integrate the snRNA-seq and SRT data by estimating the cell abundance of the snRNA-seq populations, which are used as reference populations, at each spatial location (spot) in the Visium SRT samples. This correctly mapped (A) NE neurons (cluster 6) and (B) 5-HT neurons (cluster 21) to the spatial regions where these populations were previously identified based on expression of marker genes ( and 14 ). However, the estimated absolute cell abundance of these populations per spot was higher than expected.

    Journal: bioRxiv

    Article Title: The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    doi: 10.1101/2022.10.28.514241

    Figure Lengend Snippet: We applied a spot-level deconvolution algorithm (cell2location ) to integrate the snRNA-seq and SRT data by estimating the cell abundance of the snRNA-seq populations, which are used as reference populations, at each spatial location (spot) in the Visium SRT samples. This correctly mapped (A) NE neurons (cluster 6) and (B) 5-HT neurons (cluster 21) to the spatial regions where these populations were previously identified based on expression of marker genes ( and 14 ). However, the estimated absolute cell abundance of these populations per spot was higher than expected.

    Article Snippet: The SRT data using the 10x Genomics Visium platform captures around 1-10 cells per measurement location in the human brain, and future studies could apply a higher-resolution platform to characterize expression at single-cell or sub-cellular spatial resolution.

    Techniques: Expressing, Marker

    We visualized the spatial expression of cholinergic marker genes (A) SLC5A7 and (B) ACHE in the N =9 initial Visium SRT samples, which showed that these genes were expressed both within and outside the annotated LC regions. Color scale shows UMI counts per spot.

    Journal: bioRxiv

    Article Title: The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    doi: 10.1101/2022.10.28.514241

    Figure Lengend Snippet: We visualized the spatial expression of cholinergic marker genes (A) SLC5A7 and (B) ACHE in the N =9 initial Visium SRT samples, which showed that these genes were expressed both within and outside the annotated LC regions. Color scale shows UMI counts per spot.

    Article Snippet: The SRT data using the 10x Genomics Visium platform captures around 1-10 cells per measurement location in the human brain, and future studies could apply a higher-resolution platform to characterize expression at single-cell or sub-cellular spatial resolution.

    Techniques: Expressing, Marker

    All datasets described in this manuscript are freely accessible via interactive web apps and downloadable R/Bioconductor objects (see for details). (A) Screenshot of Shiny web app providing interactive access to Visium SRT data. (B) Screenshot of iSEE web app providing interactive access to snRNA-seq data.

    Journal: bioRxiv

    Article Title: The gene expression landscape of the human locus coeruleus revealed by single-nucleus and spatially-resolved transcriptomics

    doi: 10.1101/2022.10.28.514241

    Figure Lengend Snippet: All datasets described in this manuscript are freely accessible via interactive web apps and downloadable R/Bioconductor objects (see for details). (A) Screenshot of Shiny web app providing interactive access to Visium SRT data. (B) Screenshot of iSEE web app providing interactive access to snRNA-seq data.

    Article Snippet: The SRT data using the 10x Genomics Visium platform captures around 1-10 cells per measurement location in the human brain, and future studies could apply a higher-resolution platform to characterize expression at single-cell or sub-cellular spatial resolution.

    Techniques: