--- title: "Spatial Transcriptomics" search_description: "IGATech offers high-resolution single-cell and spatial RNA sequencing to analyze gene expression at the cellular level, ideal for research in immunology, oncology, and developmental biology. Discover cell-specific insights with our advanced sequencing services." published: 2025-12-19 13:26:21.294134+00:00 locale: "en" --- # Spatial Transcriptomics [Contact Us!](https://igatechnology.com/igatech/contacts/#contact-form) ## Technologies ![NovaSeq X Plus](/media/images/Illumina_NovaSeq_XPlus_Left_561x375.width-500.png) ### NovaSeq X Plus The NovaSeq X Plus is a powerful and scalable ultra-high-throughput sequencing system that supports the broadest range of applications and study sizes. Unrivaled data quality using Illumina's proven SBS chemistry has made the NovaSeq X Plus the instrument of choice for all major genome centers and leading institutions throughout the world. Producing up to 25 billion reads \(7.5 Tbp\) per flowcell, yielding up to 120 human genomes in about 2 days at full capacity. ![AVITI Element Biosciences](/media/images/0.width-500.png) ### AVITI Element Biosciences The AVITI System by Element Biosciences is a benchtop sequencer designed for high performance, cost efficiency, and flexibility. It features dual independent flow cells for parallel or independent operation, enabling flexibility in throughput from low to full. The system utilizes Avidity Sequencing™ technology, ensuring over 90% of reads exceed Q30 quality, with minimal errors, low duplication rates, and reduced AT/GC bias. It supports easy data conversion to FASTQ files, offers compatibility with numerous assays, and provides cost-effective sequencing. This is our ideal companion for dedicated and fast-turnaround run set-up. For more detailed information, you can visit their website directly at [https://www.elementbiosciences.com/products/aviti](https://www.elementbiosciences.com/products/aviti). ![Spatial Transcriptomics](/media/images/spacial.width-500.png) ### Spatial Transcriptomics Spatial transcriptomics is a technology that maps gene expression directly within intact tissue sections, preserving the spatial context of cellular activity. Unlike bulk or single-cell RNA sequencing, which lose positional information, spatial methods reveal how cells interact within their native microenvironment. The Open-ST protocol enables scalable, high-resolution capture of mRNA transcripts over large tissue areas through an open and cost-effective workflow. This approach supports the discovery of cell–cell communication patterns, tissue architecture, and molecular gradients, advancing fields from cancer research to plant biology and neuroscience. See [Spatial Transcriptomics](/sequencing-services/spatial.md). ![spatial\_w\_clustersRNA\_segmented](/media/images/spatial_w_clustersRNA_segmented2.width-1500.png) **Whole transcriptome coverage \(unbiased gene expression\)** **Spatial resolution at subcellular level** ## Mapping gene expression in space Spatial Transcriptomics \(ST\) is a cutting-edge technique that measures gene expression within the cytoarchitecture of intact tissues. ST analyzes the spatial context of each mRNA molecule enabling both the coverage of whole transcriptome and a single-cell, even subcellular spatial resolution. In **oncology**, ST provides crucial insights on the tumor microenvironment – specifically, on how cancer cells interact with their neighboring cell types. Moreover, since failure in drug treatment is largely due to the heterogeneity of cancer cells, ST helps uncovering any response diversity by investigating cells' pharmacogenomics profiles. In **neuroscience**, ST improves the content of brain atlases by mapping which genes are active in specific regions and uncovers pathological transcription profiles across different brain circuits. In **developmental and stem biology**, ST allows to map how cell fate emerges in space and time and highlights the molecular mechanisms behind tissue regeneration at the spatial level. In addition, ST is being applied in a growing number of fields in research and medicine. ## IGATech workflow At IGATech, we offer a **cost-effective** and **high-resolution** method to provide ST services. Our method allows to reach **subcellular resolution** and being scalable to **3D**. - Sample management of **OCT-embedded** frozen tissues and **FFPE** samples - **End-to-end** analysis from raw reads to spatially resolved insights - Reconstruction of **gene expression in 3D maps** - Clear reporting and fully reproducible pipelines - For large projects and research initiatives, we can host researchers to operate cryosectioning on-site. A small pilot experiment can be organized for first-time users as a proof-of-concept: tissue capture areas can be delivered to users' labs requiring only a minimal upfront investment. Our comprehensive support covers every step: from experimental design to sample preparation and bioinformatics. **TAILORED CONSULTANCY** For every project we want to make sure that the outcome will meet your expectations ## Bioinformatics Support - **Data Processing:** quality control of transcriptomic reads and pseudo-image generation. - **Multi-Sample** **data integration** **and batch-effect** **correction** - **Cell segmentation** **and alignment** of pseudo-images with histological images. - **Clustering & Annotation:** Identification of highly variable genes, dimensionality reduction, clustering, identification of cell marker genes and cell type annotation. - **Differential** **gene** **expression** **analysis** - **Advanced and custom analysis:** regulatory networks, trajectory inference, integration with single-cell RNA sequencing data. - **Interactive data visualization tools** ## Terms and Conditions - [Privacy Information.pdf](/documents/12/Privacy_Information_rev00.pdf) - [Human samples clearance.pdf](/documents/13/__Human-samples_clearance.pdf) - [Shipping and Packaging Guidelines.pdf](/documents/9/SHIPPING_AND_PACKAGING_GUIDELINES.pdf) - [rev05 Terms and Conditions.pdf](/documents/137/__M12_01_rev05_Terms_and_Conditions.pdf)