Custom oligonucleotide probe sets for spatial transcriptomics, multiplex RNA imaging, and spatial genomics research. Bio-Synthesis supports MERFISH, seqFISH, smFISH, custom barcoded probe libraries, fluorescent labeling, conjugation chemistry, and advanced RNA imaging workflows.
Spatial transcriptomics combines gene expression analysis with spatial information, helping researchers determine where RNA molecules are located within tissues, organs and individual cells.
Unlike bulk RNA sequencing or conventional single-cell RNA sequencing, spatial transcriptomic methods preserve tissue architecture while measuring transcript abundance. This makes it possible to connect RNA expression with cellular organization, tissue microenvironments, developmental processes, immune landscapes and disease pathology.
Bio-Synthesis manufactures custom oligonucleotide probe sets for spatial transcriptomic and RNA imaging workflows, ranging from single-molecule detection to highly multiplexed spatial genomics applications. Probe sets may include direct fluorescent labels, combinatorial barcodes, sequential readout sequences, amplification domains, haptens, spacers or error-correcting encoding strategies depending on the method.
Compare MERFISH, seqFISH and smFISH probe strategies for your spatial RNA imaging goals.
Support for target-binding regions, barcode domains, readout sequences and fluorescent labels.
Custom synthesis, fluorescent labeling, conjugation chemistry, probe pools and QC documentation.
Preserve tissue architecture while measuring RNA expression and transcript localization.
Analyze RNA expression at cellular or subcellular resolution depending on the platform.
Support targeted panels through high-plex RNA imaging strategies.
Design marker panels around tissue type, disease model, pathway or cell identity.
Spatial transcriptomic probe sets are used wherever RNA expression must be interpreted within tissue structure and cellular context.
Tumor microenvironment characterization, biomarker discovery, immune infiltration studies and therapy-response mapping.
Neuronal subtype mapping, glial marker panels, brain architecture studies and disease-model profiling.
Immune-cell localization, cytokine profiling, inflammation mapping and tissue immune landscapes.
Lineage programs, organoids, tissue patterning, cell atlas projects and spatial gene-expression maps.
Spatial transcriptomics is a broad category. MERFISH, seqFISH and smFISH are related RNA imaging approaches, but each uses a different probe architecture and experimental strategy.
error-robust barcodes
sequential hybridization
single-molecule RNA
MERFISH — best for highly multiplexed spatial RNA imaging with error-correcting barcode architectures.
seqFISH — best for sequential RNA imaging using combinatorial hybridization cycles.
smFISH — best for direct visualization of individual RNA molecules with lower panel complexity.
Hybridize directly to RNA targets and define transcript specificity.
Encode transcript identity through combinatorial or sequential readout strategies.
Enable secondary fluorescent probes to bind during imaging cycles.
Generate optical signals using FAM, Cy dyes, Alexa Fluor dyes, ATTO dyes, NIR dyes and more.
Support signal amplification, library handling or workflow-specific sensitivity improvement.
Improve decoding accuracy in highly multiplexed MERFISH-like workflows.
Panel performance depends on biological target selection, probe architecture, barcode orthogonality, fluorophore strategy, sample compatibility and manufacturing feasibility.
Target Selection — choose genes that answer the biological question and distinguish cell states.
Panel Size — match panel complexity to the spatial question and imaging platform.
Barcode Design — maintain orthogonality, decoding accuracy and readout compatibility.
Fluorophore Strategy — choose dyes and conjugation chemistry around the microscope and multiplex plan.
Sample Compatibility — consider tissue processing, fixation and RNA accessibility.
Bio-Synthesis supports spatial transcriptomic probe programs beyond basic oligo synthesis, including fluorescent labels, barcodes, readout probes, haptens, spacers, custom conjugation chemistry, purification and documentation.
Need a specific dye or chemistry? If your preferred fluorophore, hapten, spacer or conjugation handle is not listed, review the full dye and labeling capabilities here: Fluorescent-Labeled Oligonucleotides.
From target selection and panel design through manufacturing, labeling, hybridization and imaging analysis.
Choose marker genes, pathways, cell types or transcript panels.
Define MERFISH, seqFISH, smFISH or custom architecture.
Synthesize probe pools, readouts, encoding probes or labeled sets.
Incorporate fluorophores, haptens, spacers or conjugation handles.
Apply probes to tissue, cells, organoids or prepared samples.
Generate spatial expression maps and transcript localization data.
→
MERFISH, seqFISH, smFISH, gene panels, barcode architecture and readout design.
Fluorescent dyes, haptens, spacers, amino/thiol handles and custom conjugation.
Spatial transcriptomic probe sets require controlled synthesis, sequence handling, labeling strategy, purification, documentation and project-specific delivery formats.
Bio-Synthesis supports custom probe pool manufacturing, fluorescent labeling, barcode/readout oligos, custom conjugation chemistry, purification, analytical QC, documentation and packaging for spatial transcriptomics and RNA imaging workflows.
Technical note: Final probe design should be evaluated within the selected platform, target gene expression, sample preparation, imaging hardware, fluorophore channels, barcode architecture and data-analysis workflow.
Trusted by biotech leaders worldwide for over 45+ years of delivering high quality, fast and scalable synthetic biology solutions.