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Biobank/preclinical models/clinical databases
- Custom made protocols for frozen and FFPE research biobank, "from patient to lab"
- Standardized procedures for storage and use of cell line models
- Standardized procedures for patient derived tumor oganoid lineages
- Detailed molecular and clinical databases
- Sensitive patient data stored at secured platforms
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Genomics & Epigenomics
- High-throughput sequencing:
- Exome, RNA, reduced-representation bisulphate sequencing (RRBS), whole genome
- Ultra-deep targeted sequencing (Illumina MiniSeq)
- Microarrays:
- Exon-resolution gene expression (Affymetrix HTA 2.0)
- DNA copy number (Affymetrix Cytoscan)
- Digital PCR (BioRad)
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Molecular pathology
- Tissue microarray construction, sectioning and autostaining
- High-throughput automated quantitative pathology imaging (Polaris and Vectra3, Akoya)
- Multiplexed immunohistochemistry
- Multispectral imaging (bright field and fluorescence)
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Functional studies
- CRISPR/Cas9
- High-throughput drug screening
- Patient-derived ex vivo cell cultures, organoids, cell lines
- Microscopy
- Confocal fluorescence microscopy
- Super-resolution and electron microscopy (in collaboration with the core facility)
- Gene expression manipulation, gene reporter and protein assays
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Bioinformatics
- High-performance computing and data storage
- Saga and Colossus (sensitive data) supercomputer clusters (provided by Sigma2 and The University of Oslo)
- Genomic data processing and quality control
- Mutation analysis, DNA methylation, gene expression, alternative splicing, fusion genes
- Multi-level data integration:
- Molecular subtyping
- Clonality modeling and tumor heterogeneity
- Effects of genomic/epigenomic changes on gene expression (including neoantigen prediction)
- Pharmacogenomics (drug sensitivity, genomics and proteomics)
- Digital image analysis
- Biostatistics
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