Excel Sheet: STOmics Validated Tissue List

STOmics Validated Tissue List

Our STOmics validated tissue list provides researchers with a comprehensive reference of hundreds of tissue types successfully tested using Stereo-seq, the cutting-edge spatial transcriptomics technology. Each tissue entry includes detailed sample information, experimental parameters, and test results, allowing scientists to make informed decisions before starting their single-cell or spatial transcriptomics experiments. By consulting this list, you can ensure compatibility with your tissue samples and streamline your experimental design.

The list not only highlights tissue types that have been validated but also provides insights into the experimental conditions that yielded the most reliable results. Researchers can leverage this information to optimize sample preparation, sequencing protocols, and data quality control measures. This reduces trial-and-error, saves valuable time and resources, and ensures reproducibility across studies. It is an essential tool for anyone planning to use Stereo-seq for spatial gene expression profiling.

In addition, our STOmics validated tissue list supports better planning for large-scale studies and comparative analyses. By providing a centralized reference for tissue performance, it helps guide tissue selection, anticipate potential challenges, and maximize experimental success. Whether you are exploring new tissue types or scaling up existing workflows, this validated tissue list is your key resource for robust, high-quality spatial transcriptomics research.

STOmics-Validated-Tissue-List

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    Notices:

    The STOmics validated tissue list was generated using standard tissue and sample types, all of which are frozen. Each tissue sample had an area of less than 1 cm² and was sectioned at a thickness of 10 μm. Most experiments were performed using the Stereo-seq Transcriptomics Kit V1.2, with a few using V1.1. Sequencing depth ranged from 1–3 G reads per sample, and data were processed using the Stereo-seq Analysis Workflow (SAW) versions V2.1.0–V5.1.3. Testing was conducted between 2020 and 2022.

    Please note that all test parameters and results are highly dependent on the tissue and sample type. This information should be used as a reference guide to help design and optimize your own experiments, rather than as definitive outcomes for all samples.

    Key parameters included in the list:

    1. MID (K): Bin200_Median_MID in thousands

    2. GENETYPE (K): Bin200_Median_Genetype in thousands

    Dr. Ebru Boslem

    ANZ Market Manager - Research Genomics

    As the official distributor in Australia and New Zealand, Decode Science makes accessing genomics solutions straightforward. Our role is to connect your lab with advanced technologies, ensuring you get the right solution for your sequencing projects—delivered locally with support when you need it.

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    Spatial Omics Analysis Suite Overview: ImageStudio, SAW, and StereoMap

    ImageStudio:

    1. ImageStudio is a SpatioTemporal omics offline image processing software.
    2. It assesses image quality, focusing on sharpness and track lines, determining suitability for downstream data analysis.
    3. The manual adjustment module addresses scenarios beyond the software’s capabilities.

    SAW (Stereo-seq Analysis Workflow):

    1. SAW integrates Stereo-seq spatial group gene expression analysis tools.
    2. It reduces and visualizes spatial expression information from sequencing data on microarrays.
    3. Spatial expression matrices generated by SAW are suitable for downstream analysis.

    StereoMap:

    1. StereoMap is a high-definition visual desktop software designed for Stereo-seq data analysis results.
    2. It visualizes STOmics’ SpatioTemporal omics technologies, allowing further exploration through various tools.
    3. GEF matrix, image RPI and IPR data, and clustering results from SAW can be displayed in StereoMap.
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    STOmics Cloud is a spatial-temporal data analysis platform for managing and analyzing multi-omics data. The platform is centered around projects, enabling users to seamlessly integrate data and tools into their projects, ensuring traceable analysis processes, reproducible results, knowledge sharing, and project collaboration. Additionally, STOmics Cloud offers a user-friendly portal interface, providing code-free data analysis, high-resolution visualization, and personalized analysis services.
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    Stereo-seq Transcriptomics for Large Chip Designs

    Stereo-seq Transcriptomics for Large Chip Designs

    STOmics Stereo-seq Transcriptomics for Large Chip Designs (LCD) pioneers the whole transcriptome study for entire tissue sections. Stereo-seq for Large Chip Designs is firstly offered to the market – 1cm x 2cm, 2cm x 2cm, 2cm x 3cm. Compatible for all species (FF samples), it enables a “tissue-to-data” solution through in situ capture of the whole transcriptome, at nanoscale resolution and centimeter-sized field of view.

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    Stereo-seq Transcriptomics H&E solution

    Unlock the potential of integrating tissue phenotyping and spatial heterogeneity profiling of molecular information. By incorporating H&E-stained tissue morphological information, Stereo-seq Transcriptomics H&E solution will better assist with tissue type identification, profiling of specific tissue regions of interests (ROIs), and conducting downstream differential analysis between selected ROIs.

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    Stereo-seq Transcriptomics mIF solution

    Stereo-seq Transcriptomics mIF solution

    STOmics Stereo-seq Transcriptomics Set for Chip-on-a-slide enables a “tissue-to-data” solution through in situ capture of the whole transcriptome, at nanoscale resolution and centimeter-sized field of view. Stereo-seq Transcriptomics Solution utilizes DNB patterned array chips loaded with spatially-barcoded probes that capture and prime poly-adenylated mRNA from tissue sections in situ. Each cDNA synthesized from mRNA captured on a particular spot is linked to its spatially-barcoded probe, allowing subsequent gene expression mapping of a tissue section following sequencing and visualization analysis using the StereoMap visualization platform.

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    Stereo-seq Transcriptomics solution

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    Stereo-seq Transcriptomics solution

    Stereo-seq Transcriptomics solution

    STOmics Stereo-seq Transcriptomics Set for Chip-on-a-slide enables a “tissue-to-data” solution through in situ capture of the whole transcriptome, at nanoscale resolution and centimeter-sized field of view. Stereo-seq Transcriptomics Solution utilizes DNB patterned array chips loaded with spatially-barcoded probes that capture and prime poly-adenylated mRNA from tissue sections in situ. Each cDNA synthesized from mRNA captured on a particular spot is linked to its spatially-barcoded probe, allowing subsequent gene expression mapping of a tissue section following sequencing and visualization analysis using the StereoMap visualization platform.

    Stereo-seq Transcriptomics solution

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    Ready To Order?
    Our team can help you in placing the order. Click below to get a quote and fast ordering.
    STOmics Kits Portfolio

    Stereo-seq Transcriptomics solution

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    Stereo-seq Transcriptomics for Large Chip Designs

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