Spatial Transcriptomics
Technologies
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