Description :
- 1. DNA Barcoding, microsatellite development. Genotyping by microsatellites analysis and sequencing
- 2. RNA/DNA sequencing: Medium throughput sequencing (ABI Prism 3130 24 capillary sequencer), high throughput short fragment sequencing (Illumina MiSeq, HiSeq 2500, NextSeq 500 & 2000, NovaSeq 6000) and long fragment sequencing (PacBio Sequel II, ONT-MinION, GridION, PromethION) in collaboration with the KU Leuven genomics platform (www.genomicscore.be).
- 3. Single-cell multi-omics analysis: Single-cell genome analysis (WGS, CNVs), Transcriptomics (10X Genomics – Chromium) and multi-omics (genome, transcriptome, epigenome) analysis. Spatial single-cell analysis (transcriptome-wide (10X Visium) & targeted (ISS/SeqFISH, VizGen, Resolve) in collaboration with the KU Leuven Single-Cell Institute for Single Cell Omics (LISCO; lisco.kuleuven.be).
- 4. Genetic marker discovery and development: development of Simple Sequence Repeats (SSRs) and Single Nucleotide polymorphisms (SNPs) with Restriction-site Associated DNA sequencing (RADseq), Genotyping by Sequencing (GBS) or Whole Genome Sequencing (deep & shallow seq).
- 5. Whole Genome assembly and Annotation: Genomics: high-quality genome assembly and functional annotation (using short & long-read technology).
- 6. Genotyping: high throughput SSR and SNP genotyping of populations, resequencing for population genomics, CNV-typing.
- 7. Population and community characterization: study of the genetic content of samples from complex environments (environmental DNA like water or soil) with metagenomics methods
- 8. Species Identification and Traceability: from low to high throughput species identification (metabarcoding with 16SrRNA (bacteria), COI (vertebrates), rbcL and matK (plants), …), tracing of individuals to the source population, pedigree validation and kinship assessment.
- 9. Gene function analysis: gene expression by in situ marker analysis (HCR, IHC) in 2D (tissue sections) and 3D (whole mount). Tissue clearing and Light-Sheet imaging. Genome and base editing by CRISPR, transgenesis.
- 10. Health Management and Molecular Parasitology: identification and quantification of pathogens in aquatic organisms using qRT-PCR, droplet digital PCR or NGS
Expertise :
RNA/DNA sequencing, Single-cell multi-omics analysis, Genetic marker discovery and development, Whole Genome assembly and Annotation, Population Genotyping and community characterization, Species Identification and Traceability, Gene function analysis, Identification and quantification of pathogens in aquatic organisms
Contact :
embrc@ugent.be, filip.volckaert@kuleuven.be