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10x Genomics Visium Spatial Transcriptome

Spatial transcriptomics is a cutting-edge technology that allows researchers to investigate gene expression patterns within tissues while preserving their spatial context. One powerful platform in this domain is 10x Genomics Visium coupled with Illumina sequencing. The principle of 10X Visium lies on a specialized chip with a designated capture area where tissue sections are placed. This capture area contains barcoded spots, each corresponding to a unique spatial location within the tissue. The captured RNA molecules from the tissue are then labeled with unique molecular identifiers (UMIs) during the reverse transcription process. These barcoded spots and UMIs enable precise spatial mapping and quantification of gene expression at a single-cell resolution. The combination of spatially barcoded samples and UMIs ensures the accuracy and specificity of the data generated. By using this Spatial Transcriptomics technology, researchers can gain a deeper understanding of the spatial organization of cells and the complex molecular interactions occurring within tissues, offering invaluable insights into the mechanisms underlying biological processes in multiple fields, including oncology, neuroscience, developmental biology, immunology, and botanical studies.

Platform: 10X Genomics Visium and Illumina NovaSeq

  • FOB Price: US $0.5 - 9,999 / Piece
  • Min.Order Quantity: 100 Piece/Pieces
  • Supply Ability: 10000 Piece/Pieces per Month
  • Service Details


    Demo Results

    Featured publications

    Technical Scheme



    ● Resolution: 100 µM

    ● Spot Diameter: 55 µM

    ● Number of spots: 4992

    ● Capture area: 6.5 x 6.5 mm

    ● Each barcoded spot is loaded with primers composed of 4 sections:

        - poly(dT) tail for mRNA priming and cDNA synthesis

        - Unique Molecular Identifier (UMI) to correct amplification bias

        - Spatial barcode

        - Binding sequence of partial read 1 sequencing primer

    ● H&E staining of sections


    ● One-stop service:  integrates all experience and skill-based steps, including cryo-sectioning, staining, tissue optimization, spatial barcoding, library preparation, sequencing and bioinformatics .

    ● Highly skilled technical team: with experience in over 250 tissue types and 100+ species including human, mouse, mammal, fish and plants.

    ● Real-time update on the entire project: with full control of experimental progress.

    ● Comprehensive standard bioinformatics:  package includes 29 analyses and 100+ high-quality figures.

    ● Customized data analysis and visualization: available for different research requests.

    ● Optional joint analysis with Single-cell mRNA sequencing


    Sample Requirements


    Sequencing strategy

    Data recommended

    Quality Control

    OCT-embedded cryo samples, FFPE samples

    (Optimal diameter: approx. 6x6x6 mm3)

    3 blocks per sample

    10X Visium cDNA library

    Illumina PE150

    50K PE reads per spot

    ( 60Gb )


    For more details on sample preparation guidance and service workflow, please feel free to talk to a 

    Service Workflow

    In the sample preparation phase, an initial bulk RNA extraction trial is performed to ensure a high-quality RNA can be obtained. In the tissue optimization stage the sections are stained and visualized and the permeabilization conditions for mRNA release from tissue are optimized. The optimized protocol is then applied during library construction, followed by sequencing and data analysis.

    The complete service workflow involves real-time updates and client confirmations to maintain a responsive feedback loop, ensuring smooth project execution.


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  • 流程图1.15-02


    Includes the following analysis:

     Data Quality Control:

    o Data output and quality score distribution

    o Gene detection per spot

    o Tissue coverage

     Inner-sample analysis:

    o Gene richness

    o Spot clustering, including reduced dimension analysis

    o Differential expression analysis between clusters: identification of marker genes

    o Functional annotation and enrichment of marker genes

     Inter-group analysis

    o Re-combination of spots from both samples (eg. diseased and control) and re-cluster

    o Identification of marker genes for each cluster

    o Functional annotation and enrichment of marker genes

    o Differential Expression of the same cluster between groups

    Inner-sample Analysis

    Spot clustering

    10x (10)


    Marker genes identification and spatial distribution


    10x (12)

    10x (11)


    Inter-group Analysis

    Data combination from both groups and re-cluster

    10x (13)



    Marker genes of new clusters


    Explore the advancements facilitated by BMKGene’s spatial transcriptomics service by 10X Visium  In these featured publications:

    Chen, D. et al. (2023) ‘mthl1, a potential Drosophila homologue of mammalian adhesion GPCRs, is involved in antitumor reactions to injected oncogenic cells in flies’, Proceedings of the National Academy of Sciences of the United States of America, 120(30), p. e2303462120. doi: /10.1073/pnas.2303462120

    Chen, Y. et al. (2023) ‘STEEL enables high-resolution delineation of spatiotemporal transcriptomic data’, Briefings in Bioinformatics, 24(2), pp. 1–10. doi: 10.1093/BIB/BBAD068.

    Liu, C. et al. (2022) ‘A spatiotemporal atlas of organogenesis in the development of orchid flowers’, Nucleic Acids Research, 50(17), pp. 9724–9737. doi: 10.1093/NAR/GKAC773.

    Wang, J. et al. (2023) ‘Integrating Spatial Transcriptomics and Single-nucleus RNA Sequencing Reveals the Potential Therapeutic Strategies for Uterine Leiomyoma’, International Journal of Biological Sciences, 19(8), pp. 2515–2530. doi: 10.7150/IJBS.83510.

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