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GENXMAP's spatial transcriptomics service combines histological imaging and next-generation sequencing (NGS) to analyze gene expression while preserving the spatial context of tissues. Unlike traditional methods that lose information about cellular organization, this innovative technology locates RNA transcripts at precise locations within the tissue architecture.
By providing a detailed view of gene expression variation between different cell types in their native environment, this service allows researchers to explore complex biological questions such as organ development, immune response, or pathological mechanisms. With GENXMAP, benefit from a powerful solution to deepen the understanding of cellular interactions and microenvironments, paving the way for meaningful discoveries in research and personalized medicine.
Pure RNA, Unlocking Precision Analysis
Reveal Spatial Expression.
Discover Spatial Gene Expression Unveiled with GENXMAP. This innovative approach captures gene expression while preserving tissue complexity, providing an accurate view of biological dynamics. Perfect for significant discoveries across various research fields.
Advantages of Spatial Transcriptomics.
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Spatial Resolution: Precise localization of gene expression, linking molecular signatures to their spatial context in the tissue.
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Tissue Preservation: Maintains the structural integrity of the tissue for a combined analysis of gene expression and histopathology.
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Heterogeneity Analysis: Identifies cellular heterogeneity and spatial variations, essential for complex tissues such as tumors or brain regions.
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Imaging/Sequencing Combination: Merging high-resolution imaging data with transcriptomic profiles for a comprehensive view of the tissue.
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Enhanced Disease Understanding: Identifies gene expression patterns linked to disease progression, offering more precise insights into tissue-specific pathology.
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Recherche sur le Cancer : Étudie les microenvironnements tumoraux pour comprendre les interactions entre différentes régions tumorales et cellules voisines.
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Neurosciences : Cartographie l'expression génique dans le cerveau, révélant la régulation spatiale associée aux différentes régions cérébrales et maladies neurologiques.
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Biologie du Développement : Analyse les changements d'expression génique au cours du développement, montrant l'organisation et la différenciation cellulaire.
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Immunologie : Étudie les réponses immunitaires et les dynamiques spatiales des cellules immunitaires.
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Découverte de Médicaments : Évalue l'impact spatial des médicaments sur les tissus, permettant de mieux comprendre les réponses thérapeutiques et les mécanismes de résistance.
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Médecine Régénérative : Examine l'organisation des cellules dans les tissus en régénération pour guider les recherches en ingénierie tissulaire et cellules souches.
Applications of Spatial Transcriptomics.
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Cancer Research: Studies the tumor microenvironments to understand interactions between different tumor regions and neighboring cells.
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Neuroscience: Maps gene expression in the brain, revealing spatial regulation associated with different brain regions and neurological diseases.
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Developmental Biology: Analyzes gene expression changes during development, showing cellular organization and differentiation.
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Immunology: Investigates immune responses and the spatial dynamics of immune cells.
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Drug Discovery: Assesses the spatial impact of drugs on tissues, allowing for a better understanding of therapeutic responses and resistance mechanisms.
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Regenerative Medicine: Examines the organization of cells in regenerating tissues to guide research in tissue engineering and stem cells.
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Recherche sur le Cancer : Étudie les microenvironnements tumoraux pour comprendre les interactions entre différentes régions tumorales et cellules voisines.
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Neurosciences : Cartographie l'expression génique dans le cerveau, révélant la régulation spatiale associée aux différentes régions cérébrales et maladies neurologiques.
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Biologie du Développement : Analyse les changements d'expression génique au cours du développement, montrant l'organisation et la différenciation cellulaire.
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Immunologie : Étudie les réponses immunitaires et les dynamiques spatiales des cellules immunitaires.
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Découverte de Médicaments : Évalue l'impact spatial des médicaments sur les tissus, permettant de mieux comprendre les réponses thérapeutiques et les mécanismes de résistance.
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Médecine Régénérative : Examine l'organisation des cellules dans les tissus en régénération pour guider les recherches en ingénierie tissulaire et cellules souches.
Optimized and Transparent Services
Our Go/No-Go processes allow you to track the progress of your project in real-time. At each stage, you validate the transition to the next, ensuring complete control and maximum transparency throughout the entire process.
Our optimized timelines ensure fast and efficient execution of each project while meeting your specific requirements. This system ensures proactive time management, minimizing delays and maximizing productivity to deliver results that align with your expectations.
Our tailored processes are designed to meet the unique needs of each project, offering flexibility and personalized follow-up. This system ensures rigorous control while delivering accurate results that align with your expectations.
Our detailed analyses guarantee reliable and in-depth results tailored to each study. With cutting-edge tools and proven methodologies, we provide a precise understanding of genetic data, while adhering to the highest standards of quality and scientific rigor.
Service Details
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We clearly define your scientific objectives to guide your study:
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Identification of Research Objectives: You will outline your scientific objectives, allowing us to understand the goals of your study.
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Identification of Sample Types: You will specify the types of samples you wish to analyze, enabling us to tailor the preparation and sequencing process. We offer guidance from the fixation of your sample.
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Budget and Timeline Estimation
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Budget Validation: We provide a clear cost estimate based on the chosen methodology, the number of samples, the required coverage, and additional bioinformatics analysis.
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Timeline Planning: An estimated timeline for sample preparation, sequencing, and bioinformatics analysis is shared, with regular checkpoints to track progress.
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Ongoing Support and Follow-up
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Continuous Support: Once the project is launched, we assist you throughout the process, from raw data collection to bioinformatics support for interpreting results, providing personalized reports and recommendations for the next steps.
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High-Throughput Sequencing (Next-Generation Sequencing - NGS): GENXMAP uses the following platforms:
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NovaSeq (Illumina)
Advantages:
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Fast and accurate sequencing of large amounts of DNA from various environmental or biological sources.
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Provides high coverage and depth for precise detection of microorganisms present.
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MiSeq (Illumina)
Advantages:
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High precision: Illumina’s synthesis sequencing technology is known for its low error rate, making it ideal for analyses requiring great accuracy, such as genetic variation studies.
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Rapid turnaround: Quick run times enable timely results for urgent projects.
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Oxford Nanopore Technology (ONT)
Advantages:
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Long reads: ONT allows for the generation of very long reads (up to several hundred kb), which is valuable for studying complex genomic regions, whole genomes, and full-length transcripts without fragmentation.
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Real-time data: Immediate analysis during sequencing, providing instant insights.
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Step 0 >> Sample Reception Check:
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Visual evaluation for quantity and quality.
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Report and client decision "Go/No-Go" for the continuation of the process.
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Step 1 >> Sample Preparation:
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Extraction of the tissue of interest (e.g., biopsies, organs, etc.).
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Rapid tissue fixation to preserve cellular architecture (e.g., using paraformaldehyde).
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Tissue sectioning into thin slices (typically 5-10 µm) using a microtome or cryostat.
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Step 2 >> Histological Imaging:
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Perform histological imaging to visualize tissue structure and assist in mapping areas of interest for analysis.
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Staining sections to better distinguish different tissue structures.
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Step 3 >> Spatial RNA Capture:
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Place tissue sections on a special capture surface (such as a chip or membrane with specific probes for each region).
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Capture RNA transcripts present in the tissue and associate them with spatial barcodes to maintain localization information.
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Step 4 >> RNA Extraction and Reverse Transcription:
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Extract the captured RNA and convert it into complementary DNA (cDNA) through reverse transcription.
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Mark cDNA with specific barcodes corresponding to their locations in the tissue.
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Step 5 >> cDNA Amplification:
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Amplify the cDNA to increase the amount of genetic material ready for sequencing.
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Step 6 >> Data Analysis:
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Sequencing Library Construction:
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Prepare the library by adding necessary adapters for sequencing, allowing identification of transcripts and their position in the tissue.
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Step 7 >> Sequencing:
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Sequence the cDNA library using high-throughput sequencing platforms (e.g., Illumina).
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Step 8 >> Data Analysis:
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Data Quality Control:
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Verify the quality of the sequences (identify low-quality cells or areas, remove artifacts).
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Assess transcript coverage and integrity.
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Data Filtering:
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Eliminate dead or low-quality cells.
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Normalize data to account for technical biases (e.g., capture or sequencing effects).
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Spatial Mapping:
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Assign transcripts to their specific positions in the tissue using spatial barcodes.
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Visualize data as gene expression maps using spatial visualization tools.
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Dimensionality Reduction:
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Apply methods such as PCA, t-SNE, or UMAP to reduce data complexity and visualize gene expression variation in the tissue.
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Cellular Clustering:
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Identify groups of cells with similar gene expression profiles, considering their position in the tissue.
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Define subpopulations of cells and explore their functional roles.
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Differential Analysis:
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Compare gene expression between different areas or cell types of the tissue.
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Identify genes differentially expressed across spatial regions.
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Cell Type Annotation:
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Identify and assign cell types based on their gene expression profiles.
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Use known databases or markers to annotate present cell types.
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Cellular Interactions Analysis:
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Study interactions between cells through ligands and receptors (using tools such as CellPhoneDB or CellChat).
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Explore microenvironments and spatial interaction networks.
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Pathways and Functional Analysis:
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Identify biological pathways and functional processes associated with specific tissue regions.
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Enhance analyses using pathway databases such as KEGG, Reactome, or GO.
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Cellular Trajectories (Pseudotime):
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Study cellular transitions, e.g., during differentiation or stress responses, using algorithms such as Monocle or Slingshot.
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For more information, feel free to visit our "Bioinformatics & Biostatistics Analysis" page.
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Step 9 >> Result Delivery:
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Result Formats: Provide raw files (FASTQ), assemblies, taxonomic results, functional analyses, and metadata.
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Detailed Report: Includes a summary of results, visualizations (graphs, phylogenetic trees), biological interpretation, and recommendations for next steps.
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Delivery Methods: Access via a secure online platform, email delivery, or a results presentation meeting.
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Follow-up and Support: Post-delivery assistance for clarifications, revisions, or additional analyses.
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Delivery Time: Typically between 3 to 6 weeks, depending on the complexity of the project.
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GENXMAP, your trusted partner to support you in your research.
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