Applications
At the Genomics Facility Basel, we support a wide range of applications in transcriptomics, genomics, and epigenomics. Our team is highly flexible and works closely with researchers to tailor protocols to their specific scientific questions and sample types.
There is no one-size-fits-all recipe! We adapt our workflows to your needs — from input quality and quantity to the biological question at hand.
Let’s Talk!
Not sure which application fits your project? We’re happy to discuss your needs and help design the best approach. We encourage you to reach out before starting your experiments.
Contact us at to schedule a consultation.
Genomics
From whole genomes to targeted panels, we support a wide range of DNA sequencing applications:
- Whole Genome Sequencing (WGS), including PCR-free protocols
- Whole Exome Sequencing (WES), automated with Agilent Bravo Workstation
- Targeted Sequencing – Custom enrichment panels, Amplicon sequencing, 16S rRNA gene sequencing
- single-cell/nucleus DNA-seq for CNV and SNV detection in single cells
Transcriptomics
We offer comprehensive solutions for studying gene expression at bulk and single-cell resolution:
- Bulk RNA-seq – For whole-tissue or population-level transcriptome profiling (incl. metatranscriptomics)
- Single-cell/nucleus RNA-seq – scRNA-seq, scATAC-seq, Multiome (scRNA + scATAC), snRNA-seq
- Small RNA-seq – miRNA-seq, piRNA, siRNA, and other small RNA species
Epigenomics
Explore chromatin accessibility, DNA methylation, and protein-DNA interactions:
- ATAC-seq
- ChIP-seq
- CUT&RUN/TAG
- Whole Genome Methylation Profiling
Single-cell and Spatial (multi-)omics
Explore cellular features on single-cell level and/or within their spatial context
- Gene expression profiling at single-cell resolution and TCR/BCR sequencing
- Multiome gene expression + chromatin accessibility (ATAC-seq)
- Combine gene expression and cell surface profiling with functional CRISPR screening
- Characterize tumor heterogeneity by means of single-cell SNV and/or CNV detection
- Single-cell transcript isoform sequencing
Library Preparation & Quality Control
We offer customized library preparation based on your input material and research goals.
Already prepared your libraries? You're welcome to submit them! We accept user-prepared libraries for all applications including CLIP-seq, RAD-seq, ATAC-seq, Hi-C and others
Before sequencing, we perform rigorous QC to ensure high-quality data:
- Fragment analysis: Fragment Analyzer, TapeStation, Bioanalyzer
- Concentration measurements: Qubit assays, PicoGreen, RiboGreen
We also offer library pooling and index balancing as part of our service.