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10X Genomics visium spatial tissue optimization
Visium Spatial Tissue Optimization, 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+spatial+tissue+optimization/expression+gene+slides+spatial+visium/pm42097141-296-1-5
Average 86 stars, based on 1 article reviews
visium spatial tissue optimization - by Bioz Stars, 2026-11
86/100 stars

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Related Articles

Gene Expression:

Article Title: Mapping neuro-vascular unit communications reveals distinct angiogenic programs across developing mouse brain regions.
Article Snippet: .. Reactions were carried out with the Visium Spatial Gene Expression (GEX) and Tissue Optimization (TO) Slide & Reagent Kits according to the manufacturer’s protocol with recommended reagents (10X Genomics, 1000193 and 1000187). ..

Article Title: A glycan-based adjuvant expands the breadth and duration of protection of mRNA-based vaccines.
Article Snippet: DLS (ZetaPlus Zeta Potential Analyzer; Brookhaven Instruments) was performed to determine the stability of each active pharmaceutical ingredient in the FDC solution. .. 5′ gene expression (GEX) libraries, single-cell V(D)J libraries (10x Genomics, 1000255) and cell surface protein libraries were prepared according to the manufacturer’s protocols. .. Library quality was evaluated using an Agilent 2200 TapeStation, and final libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina platforms.

Article Title: WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm.
Article Snippet: 10,000 nuclei per sample were processed and isolated using the Nuclei EZ Prep kit (Sigma-Aldrich) according to the manufacturer’s protocol. .. Libraries for both ATAC-seq and RNA-seq were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283). .. Cells were first stained for aldehyde dehydrogenase expression using the ALDEFLUOR Kit (StemCell Technologies, Cat# 01700) according to the manufacturer’s protocol.

Single Cell:

Article Title: A glycan-based adjuvant expands the breadth and duration of protection of mRNA-based vaccines.
Article Snippet: DLS (ZetaPlus Zeta Potential Analyzer; Brookhaven Instruments) was performed to determine the stability of each active pharmaceutical ingredient in the FDC solution. .. 5′ gene expression (GEX) libraries, single-cell V(D)J libraries (10x Genomics, 1000255) and cell surface protein libraries were prepared according to the manufacturer’s protocols. .. Library quality was evaluated using an Agilent 2200 TapeStation, and final libraries were quantified by qPCR using the KAPA Library Quantification Kit for Illumina platforms.

Article Title: Multilayer network approaches to omics data integration in digital twins for cancer research
Article Snippet: .. This process requires the non-trivial development of new methods that capture salient information from either estimation of cell type proportions from bulk RNA-seq , or from single-cell spatial (Visium/Xenium) ( ) and non-spatial datasets (10x Genomics scRNA-seq/scATAC-seq) ( ). ..

Article Title: WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm.
Article Snippet: 10,000 nuclei per sample were processed and isolated using the Nuclei EZ Prep kit (Sigma-Aldrich) according to the manufacturer’s protocol. .. Libraries for both ATAC-seq and RNA-seq were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283). .. Cells were first stained for aldehyde dehydrogenase expression using the ALDEFLUOR Kit (StemCell Technologies, Cat# 01700) according to the manufacturer’s protocol.

RNA Sequencing:

Article Title: Multilayer network approaches to omics data integration in digital twins for cancer research
Article Snippet: .. This process requires the non-trivial development of new methods that capture salient information from either estimation of cell type proportions from bulk RNA-seq , or from single-cell spatial (Visium/Xenium) ( ) and non-spatial datasets (10x Genomics scRNA-seq/scATAC-seq) ( ). ..

Article Title: WNT signaling in human pluripotent stem cells promotes HDAC2-dependent epigenetic programs and development of retinoic acid-responsive mesoderm.
Article Snippet: 10,000 nuclei per sample were processed and isolated using the Nuclei EZ Prep kit (Sigma-Aldrich) according to the manufacturer’s protocol. .. Libraries for both ATAC-seq and RNA-seq were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics, PN-1000283). .. Cells were first stained for aldehyde dehydrogenase expression using the ALDEFLUOR Kit (StemCell Technologies, Cat# 01700) according to the manufacturer’s protocol.

other:

Article Title: Melanoma cell states shape spatial tumor-immune ecosystems to dictate the efficacy of anti-PD1 immunotherapy.
Article Snippet: Spatial transcriptomic data were generated by the CRCL (Cancer Research Center Of Lyon) Cancer Genomics Platform using Visium CytAssist Spatial gene expression for FFPE, Human Transcriptome, kit (10X Genomics), according to the manufacturer’s guidelines.



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Web summary metrics generated from 10× Genomics SpaceRanger Web summaries generated from 10× Genomics Space Ranger pipeline after receiving raw data for P0 mouse tissue in <t>Visium</t> spatial transcriptomics step. The summary page will provide detailed information regarding data quality including “Fraction Reads in Spots Under Tissue”. To determine localization of diffused RNA and confirm that RNA is “leaking” from tissue section, rerun Space Ranger on all spots in the Visium capture area. If Fraction Reads in Spots Under Tissue is below 50%, optimization is required. (A) Unsuccessful reads in spots are most likely due to <t>over</t> <t>permeabilization</t> when releasing RNA. (B) Successful processing of P0 tissue with 10× Visium.
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( A ) Comparison of SERPINE1 expression in SSc and healthy control skin biopsy samples from the GEO dataset ( GSE58095 ). ( B ) Correlation analysis of modified Rodnan skin scores (mRSS) versus SERPINE1 expression from the data in A . ( C ) Enriched signature for expression of extracellular matrix (ECM) genes along with expression of the myofibroblast marker COL8A1 , and SERPINE1 (PAI-1) expression in SSc skin on <t>the</t> <t>10x</t> <t>Visium</t> spatial platform (data representative of n = 4). ( D ) Violin plots of SERPINE1 expression in controls versus SSc skin across single-cell RNA-seq data from different cellular populations (top) and fibroblast subsets (bottom) ( n = 18 healthy controls, n = 22 SSc patients). ( E ) Enriched biological processes in SERPINE1 + versus SERPINE1 – COL8A1 myofibroblasts. ( F ) IHC of PAI-1 in SSc skin biopsy (data representative of n = 6). ( G ) IHC of PAI-1 in skin biopsy from a healthy volunteer. Scale bars: 500 μm on overall biopsy, 50 μm on the insets. **** P < 0.0001 by 2-tailed Mann-Whitney test in A . P = 0.0003 by Spearman’s r correlation test in B .
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( A ) Comparison of SERPINE1 expression in SSc and healthy control skin biopsy samples from the GEO dataset ( GSE58095 ). ( B ) Correlation analysis of modified Rodnan skin scores (mRSS) versus SERPINE1 expression from the data in A . ( C ) Enriched signature for expression of extracellular matrix (ECM) genes along with expression of the myofibroblast marker COL8A1 , and SERPINE1 (PAI-1) expression in SSc skin on <t>the</t> <t>10x</t> <t>Visium</t> spatial platform (data representative of n = 4). ( D ) Violin plots of SERPINE1 expression in controls versus SSc skin across single-cell RNA-seq data from different cellular populations (top) and fibroblast subsets (bottom) ( n = 18 healthy controls, n = 22 SSc patients). ( E ) Enriched biological processes in SERPINE1 + versus SERPINE1 – COL8A1 myofibroblasts. ( F ) IHC of PAI-1 in SSc skin biopsy (data representative of n = 6). ( G ) IHC of PAI-1 in skin biopsy from a healthy volunteer. Scale bars: 500 μm on overall biopsy, 50 μm on the insets. **** P < 0.0001 by 2-tailed Mann-Whitney test in A . P = 0.0003 by Spearman’s r correlation test in B .
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Image Search Results


Web summary metrics generated from 10× Genomics SpaceRanger Web summaries generated from 10× Genomics Space Ranger pipeline after receiving raw data for P0 mouse tissue in Visium spatial transcriptomics step. The summary page will provide detailed information regarding data quality including “Fraction Reads in Spots Under Tissue”. To determine localization of diffused RNA and confirm that RNA is “leaking” from tissue section, rerun Space Ranger on all spots in the Visium capture area. If Fraction Reads in Spots Under Tissue is below 50%, optimization is required. (A) Unsuccessful reads in spots are most likely due to over permeabilization when releasing RNA. (B) Successful processing of P0 tissue with 10× Visium.

Journal: STAR Protocols

Article Title: Protocol to evaluate mouse brain spatial cell type-resolved transcriptomic discoveries using 10× Visium spatial transcriptomics and FLEX scRNA-seq

doi: 10.1016/j.xpro.2025.104277

Figure Lengend Snippet: Web summary metrics generated from 10× Genomics SpaceRanger Web summaries generated from 10× Genomics Space Ranger pipeline after receiving raw data for P0 mouse tissue in Visium spatial transcriptomics step. The summary page will provide detailed information regarding data quality including “Fraction Reads in Spots Under Tissue”. To determine localization of diffused RNA and confirm that RNA is “leaking” from tissue section, rerun Space Ranger on all spots in the Visium capture area. If Fraction Reads in Spots Under Tissue is below 50%, optimization is required. (A) Unsuccessful reads in spots are most likely due to over permeabilization when releasing RNA. (B) Successful processing of P0 tissue with 10× Visium.

Article Snippet: Permeabilization time is determined with Visium Spatial Tissue Optimization (protocol CG000238) which needs to be performed before starting Spatial Transcriptomics Tissue Processing.

Techniques: Generated

( A ) Comparison of SERPINE1 expression in SSc and healthy control skin biopsy samples from the GEO dataset ( GSE58095 ). ( B ) Correlation analysis of modified Rodnan skin scores (mRSS) versus SERPINE1 expression from the data in A . ( C ) Enriched signature for expression of extracellular matrix (ECM) genes along with expression of the myofibroblast marker COL8A1 , and SERPINE1 (PAI-1) expression in SSc skin on the 10x Visium spatial platform (data representative of n = 4). ( D ) Violin plots of SERPINE1 expression in controls versus SSc skin across single-cell RNA-seq data from different cellular populations (top) and fibroblast subsets (bottom) ( n = 18 healthy controls, n = 22 SSc patients). ( E ) Enriched biological processes in SERPINE1 + versus SERPINE1 – COL8A1 myofibroblasts. ( F ) IHC of PAI-1 in SSc skin biopsy (data representative of n = 6). ( G ) IHC of PAI-1 in skin biopsy from a healthy volunteer. Scale bars: 500 μm on overall biopsy, 50 μm on the insets. **** P < 0.0001 by 2-tailed Mann-Whitney test in A . P = 0.0003 by Spearman’s r correlation test in B .

Journal: JCI Insight

Article Title: A potent inhibitor of PAI-1, MDI-2517, mitigates disease severity in a preclinical systemic sclerosis model

doi: 10.1172/jci.insight.195005

Figure Lengend Snippet: ( A ) Comparison of SERPINE1 expression in SSc and healthy control skin biopsy samples from the GEO dataset ( GSE58095 ). ( B ) Correlation analysis of modified Rodnan skin scores (mRSS) versus SERPINE1 expression from the data in A . ( C ) Enriched signature for expression of extracellular matrix (ECM) genes along with expression of the myofibroblast marker COL8A1 , and SERPINE1 (PAI-1) expression in SSc skin on the 10x Visium spatial platform (data representative of n = 4). ( D ) Violin plots of SERPINE1 expression in controls versus SSc skin across single-cell RNA-seq data from different cellular populations (top) and fibroblast subsets (bottom) ( n = 18 healthy controls, n = 22 SSc patients). ( E ) Enriched biological processes in SERPINE1 + versus SERPINE1 – COL8A1 myofibroblasts. ( F ) IHC of PAI-1 in SSc skin biopsy (data representative of n = 6). ( G ) IHC of PAI-1 in skin biopsy from a healthy volunteer. Scale bars: 500 μm on overall biopsy, 50 μm on the insets. **** P < 0.0001 by 2-tailed Mann-Whitney test in A . P = 0.0003 by Spearman’s r correlation test in B .

Article Snippet: Optimization of tissue permeabilization was performed on 20 μm sections using a Visium Spatial Tissue Optimization Reagents Kit (10x Genomics), which established an optimal permeabilization time of 9 minutes.

Techniques: Comparison, Expressing, Control, Modification, Marker, Single Cell, RNA Sequencing, MANN-WHITNEY