Name and Surname of the Supervisor: Rūta Matulevičiūtė
Institution (Company), Department: EMBL PI
Preliminary Topic: Optimising sgRNAs for HIF Targets in PDAC via In Vitro Cas9 Cleavage Assay
Short Description of the Internship Work: As part of a broader effort to study hypoxia pathways in pancreatic ductal adenocarcinoma (PDAC) cell lines, this BSc project benchmarks the in vitro cleavage efficiency of sgRNAs targeting HIF1A, EPAS1 (HIF2A), and HIF3A to inform later single-, double-, and triple-knockout designs. The student will generate sgRNAs by designing and cloning guide sequences into T7-promoter plasmid templates, then transcribe them in vitro and assemble Cas9–sgRNA RNPs. Candidate sgRNAs—selected from the literature and design tools—will be assayed on PCR amplicons spanning each target site in single-tube reactions and quantified by gel and automated electrophoresis to compute the fraction cleaved versus uncut. Deliverables are a ranked sgRNA list per gene and recommended single-/double-/triple-guide sets for follow-up.
Qualification Requirements (Degree): BSc
Application Deadline: 2026-02-05
Additional Comments: It is assumed that the student will have a good understanding of the basic theory and principles of the methods: molecular cloning, work with bacteria (transformation, colony selection), PCR and the operation of the CRISPR–Cas9 system (sgRNA design, RNP complexes, target cutting logic).