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biomark system  (fluidigm)


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    fluidigm biomark system
    Biomark System, supplied by fluidigm, used in various techniques. Bioz Stars score: 96/100, based on 3825 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/single-cell+spatial+transcriptomics+data/Biomark/pmc04655073-1-5-4
    Average 96 stars, based on 3825 article reviews
    biomark system - by Bioz Stars, 2026-11
    96/100 stars

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    Related Articles

    Polymerase Chain Reaction:

    Article Title: Identification of Candidate Causal Polymorphisms in GGT1 and SLC5A1 Associated with Fat Area Ratio on BTA17 in Japanese Black Cattle
    Article Snippet: .. The selected polymorphisms were genotyped in the Hyogo population (n = 432) using either the BiomarkTM HD system (Standard BioTools, South San Francisco, CA, USA) or the Kompetitive Allele Specific PCR (KASP) assay (LGC Genomics, Hoddesdon, UK). https://doi.org/10.3390/genes17040363 Primer and probe sequences used for genotyping are listed in Table S1. ..

    Real-time Polymerase Chain Reaction:

    Article Title: MicroRNA signatures of equine asthma endotypes in serum and bronchoalveolar lavage fluid
    Article Snippet: Subsequently, the optimal number of preamplification cycles and the number of points in the standard curve were determined using a FlexSix IFC chip (Fluidigm) according to manufacturer’s protocol. .. Following optimization, the complete qPCR experiment was performed using two 96×96 IFC chips on the BioMarkTM HD system (Fluidigm) — one chip for BALF samples, and one for serum samples, respectively. .. All cDNA samples were pre-amplified for 20 cycles, exonuclease treated and diluted 8× in TE buffer prior to running in two 96×96 IFC chips in the BioMarkTM HD system following standard Fluidigm protocols.

    Gene Expression:

    Article Title: A naturalized gut microbiome interacts with dietary fibers to protect against colonic inflammation.
    Article Snippet: .. Relative gene expression analysis of colonic mucosa RT‒qPCR was applied to colonic mucosa RNA using BiomarkTM HD (Standard Biotools Inc.) and an intestinal barrier gene panel of 37 target genes previously validated 16 following the manufacturer's protocol. .. Briefly, cDNA was prepared using Reverse Transcription Master Mix (Standard Biotools Inc., #100-6298) with 20 ng/μL RNA.

    Article Title: Prostate neoantigens and their uses
    Article Snippet: 37.5 ng cDNA was preamplified with gene markers in 15 μl preamplification mix using TaqMan preamplification kit (ThermoFisher Scientific) and standard protocols. .. To test gene expression of the identified neoantigens in the various samples, primers spanning the breakpoint sequences were designed for each of the identified prostate neoantigens and expression was assessed using Fluidigm BiomarkTM HD. ..

    Immunopeptidomics:

    Article Title: Prostate neoantigens and their uses
    Article Snippet: 37.5 ng cDNA was preamplified with gene markers in 15 μl preamplification mix using TaqMan preamplification kit (ThermoFisher Scientific) and standard protocols. .. To test gene expression of the identified neoantigens in the various samples, primers spanning the breakpoint sequences were designed for each of the identified prostate neoantigens and expression was assessed using Fluidigm BiomarkTM HD. ..

    Expressing:

    Article Title: Prostate neoantigens and their uses
    Article Snippet: 37.5 ng cDNA was preamplified with gene markers in 15 μl preamplification mix using TaqMan preamplification kit (ThermoFisher Scientific) and standard protocols. .. To test gene expression of the identified neoantigens in the various samples, primers spanning the breakpoint sequences were designed for each of the identified prostate neoantigens and expression was assessed using Fluidigm BiomarkTM HD. ..



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    Image Search Results


    (a) Simplified cross-section of the human epidermis, highlighting squamous cells, melanocytes and basal cells. Coloured regions represent cSCC (green), which originates from squamous cells, melanoma (orange), which originates from melanocytes, and BCC (blue), which originates from basal cells. Two orange melanocytes are shown in the dermal region as occurs in invasive melanoma; other cells in the lower dermis layer are not depicted. (b) Overview of sample design and technologies used to generate data for this project. ROI - region of interest; FOV - field of view; S - cSCC; B - BCC; M - melanoma; HC - healthy (cancer patient); HNC - healthy (non-cancer patient donor). Technologies included are single cell RNA sequencing for fresh samples, single nuclei sequencing for formalin-fixed samples, Visium, Xenium, CosMX, GeoMX DSP for whole transcriptome, GeoMX DSP for proteins, Polaris, RNAscope, the proximal ligation assay, spatial glycomics and CODEX.

    Journal: bioRxiv

    Article Title: Integrating 12 Spatial and Single Cell Technologies to Characterise Tumour Neighbourhoods and Cellular Interactions in three Skin Cancer Types

    doi: 10.1101/2025.07.25.666708

    Figure Lengend Snippet: (a) Simplified cross-section of the human epidermis, highlighting squamous cells, melanocytes and basal cells. Coloured regions represent cSCC (green), which originates from squamous cells, melanoma (orange), which originates from melanocytes, and BCC (blue), which originates from basal cells. Two orange melanocytes are shown in the dermal region as occurs in invasive melanoma; other cells in the lower dermis layer are not depicted. (b) Overview of sample design and technologies used to generate data for this project. ROI - region of interest; FOV - field of view; S - cSCC; B - BCC; M - melanoma; HC - healthy (cancer patient); HNC - healthy (non-cancer patient donor). Technologies included are single cell RNA sequencing for fresh samples, single nuclei sequencing for formalin-fixed samples, Visium, Xenium, CosMX, GeoMX DSP for whole transcriptome, GeoMX DSP for proteins, Polaris, RNAscope, the proximal ligation assay, spatial glycomics and CODEX.

    Article Snippet: Cells expressing the two genes are visualized on single-cell level resolution spatial data from STOmics and Curio-Seeker (Takara Bio, USA) melanoma samples and appear to be in spatial proximity ( ).

    Techniques: RNA Sequencing, Sequencing, RNAscope, Ligation

    (a) Gene specificity score (GSS) and association of spatial spots with skin cancer heritability. GSS score for each gene in a spot/cell represents the enrichment of the gene as a top rank most abundant gene in the spot/cell and its neighbour spots/cells in an anatomical region, a spatial domain, or a cell type. The p-value shows the spatial heritability enrichment significance of a spot with a trait based on SNPs mapped to the genes with high GSS scores (one-sided Z-test for stratified coefficient different to 0). The p-value is more significant if the SNPs that are mapped to the high GSS genes explain a higher proportion of heritability for the trait. (b) Cell types with the highest enrichment of heritability explained by SNPs tagged to GSS genes of cells in a cell type. The white asterisks indicate the most enriched cell-type for heritability of cutaneous melanoma, cSCC and BCC traits. (c) gsMAP significance spatial heritability enrichment is shown at single-cell resolution across the tissue (upper tissue plots) or per annotated skin regions (lower violin plots) from the cosMx data of the sample mel48974. (d) LR pairs with significant association with SNP heritability explained by the corresponding cell types. The rectangles show cases where both L and R genes had PCC >0.3 between GSS of the gene and the gsMAP P-values (the significance level for the LD stratified coefficients for the spot bigger than 0). The results suggest which LR pairs are related with the heritability of a cell type pairs. (e) GSS of two LR pairs showing specificity of the L and R genes to tissue regions at the immune-rich dermal layers and the epidermis of the skin. (f) Manhattan plot showing top significant GWAS SNPs co-localizing with genes in melanocytes (red) and T cells (blue) that had the highest Pearson correlation between GSS and the gsMAP trait association P-value or associated with SNPs with genome-wide significance. The Y-axis shows the -log(P-value) from GWAS analysis.

    Journal: bioRxiv

    Article Title: Integrating 12 Spatial and Single Cell Technologies to Characterise Tumour Neighbourhoods and Cellular Interactions in three Skin Cancer Types

    doi: 10.1101/2025.07.25.666708

    Figure Lengend Snippet: (a) Gene specificity score (GSS) and association of spatial spots with skin cancer heritability. GSS score for each gene in a spot/cell represents the enrichment of the gene as a top rank most abundant gene in the spot/cell and its neighbour spots/cells in an anatomical region, a spatial domain, or a cell type. The p-value shows the spatial heritability enrichment significance of a spot with a trait based on SNPs mapped to the genes with high GSS scores (one-sided Z-test for stratified coefficient different to 0). The p-value is more significant if the SNPs that are mapped to the high GSS genes explain a higher proportion of heritability for the trait. (b) Cell types with the highest enrichment of heritability explained by SNPs tagged to GSS genes of cells in a cell type. The white asterisks indicate the most enriched cell-type for heritability of cutaneous melanoma, cSCC and BCC traits. (c) gsMAP significance spatial heritability enrichment is shown at single-cell resolution across the tissue (upper tissue plots) or per annotated skin regions (lower violin plots) from the cosMx data of the sample mel48974. (d) LR pairs with significant association with SNP heritability explained by the corresponding cell types. The rectangles show cases where both L and R genes had PCC >0.3 between GSS of the gene and the gsMAP P-values (the significance level for the LD stratified coefficients for the spot bigger than 0). The results suggest which LR pairs are related with the heritability of a cell type pairs. (e) GSS of two LR pairs showing specificity of the L and R genes to tissue regions at the immune-rich dermal layers and the epidermis of the skin. (f) Manhattan plot showing top significant GWAS SNPs co-localizing with genes in melanocytes (red) and T cells (blue) that had the highest Pearson correlation between GSS and the gsMAP trait association P-value or associated with SNPs with genome-wide significance. The Y-axis shows the -log(P-value) from GWAS analysis.

    Article Snippet: Cells expressing the two genes are visualized on single-cell level resolution spatial data from STOmics and Curio-Seeker (Takara Bio, USA) melanoma samples and appear to be in spatial proximity ( ).

    Techniques: Genome Wide

    Journal: Cell

    Article Title: Spatiotemporal analysis of human intestinal development at single-cell resolution

    doi: 10.1016/j.cell.2020.12.016

    Figure Lengend Snippet:

    Article Snippet: STAR-FINDer Single Cell and Spatial Transcriptomics Data Portal , This study , https://simmonslab.shinyapps.io/FetalAtlasDataPortal.

    Techniques: Conjugation Assay, Recombinant, Saline, Modification, Plasmid Preparation, Gene Expression, RNAscope, Generated, Software