To expand our understanding of genome structure and function we have a suite of lab infrastructure where we can perform various genomic analyses. Core activities include sequencing and genotyping, functional genomic assays and gene editing.
Sequencing and genotyping
Extraction of DNA or RNA
Genomic analyses typically begins with the extraction of DNA or RNA. We have experience with a variety of single-sample and high-throughput kits and processes for DNA and RNA extraction, quantification and quality checking. This includes kits specifically aimed at extracting high molecular weight DNA fragments.
Related lab equipment:
|Platereader||Spectra Max M2e||Molecular Devices||Click here|
|NanoDrop||Nano Drop 8000||Thermo Scientific||Click here|
|Bioanalyzer||Agilent 2100||Agilent Technologies||Click here|
|QIAxcel||QIAxcel Advanced||Qiagen||Click here|
|SpeedVac||SPD111V||Thermo Scientific||Click here|
|DNA size selector||BluePippin||Sage Science||Click here|
For sequencing DNA or RNA we have both short-read technology (Illumina MiSeq) and long-read technologies (Oxford Nanopore MinION and PromethION). Its relatively low output, but high accuracy, makes the MiSeq ideally suited to sequencing RNA libraries, amplicons or reduced complexity libraries, or DNA from organisms with smaller genomes. Our PromethION (the first in Norway) performs single molecule sequencing and is designed to generate long reads (>100Kb). This revolutionary technology offers great advantages for de novo sequencing, detecting structural variation and sequencing through repetitive DNA. Strategies for detecting methylation and for targeted re-sequencing of genome regions of particular interest are also available. For RNA, the technology enables direct sequencing of mRNA without PCR, and creates opportunities to detect transcript variants and base modifications.
Related lab equipment
|PromethION||PromethION 48||Oxford Nanopore Tech||Click here|
Single Nucleotide Polymorphisms (SNPs) can be used to quickly and cheaply gain insight into an individual’s genetic composition and can be used for performing GWAS, Genomic Selection, pedigree assignment etc. Our Agena Bioscience Mass Array system offers maximum design flexibility for assaying small numbers of custom SNPs (1-40) in a 384-sample format. In contrast, our Affymetrix Gene Titan systems are designed for high-resolution testing of many SNPs (50,000 – 500,000 SNPs) in 96- and 384-sample format. Both platforms are highly automated allowing us to process upwards of 450,000 samples every year.
Related lab equipment:
|Affymetrix Gene Titans||Gene Titan||Thermo Fisher Scientific||Click here|
|Automated liquid handlers||Biomek Fxp and i7||Beckman Coulter||Click here|
|MassArray4||MassArray Analyzer4||Agena Bioscience||Click here|
|Automated liquid handlers||Biomek NxpMC/i5 S8||Beckman Coulter||Click here|
Functional Genomic assays
Recognizing the function of a DNA sequence is critical in order to understand the significance of the genetic variation it contains. By sequencing RNA, it is relatively easy to distinguish those DNA sequences coding for genes, but by using functional genomics it is possible to identify regions of DNA involved in gene-regulation and bring non-coding DNA to life. Different protocols allow different facets of the genome to be explored.
ATAC-Seq (assay for transposon accessible chromatin) reveals the DNA sequences exposed when chromatin becomes relaxed, this physical change is necessary before transcription factors can bind and exert their effect on gene expression.
ChIP-Seq (Chromatin Immunoprecipitation Sequencing) allows us to detect the DNA sequences associated with modified (methylated) histones or serving as binding sites for specific transcription factors.
Hi-C allows us to explore the organization (conformation) of DNA within cells by isolating pairs of DNA sequences that are nearby in 3D space. Physical associations between loci that are far apart in linear DNA can indicate promoter-enhancer interaction and be used to identify topologically associated domains (regions of sequence showing significant interactivity). Since physical associations tend to erode over longer (Mb) distances and are rare between chromosomes, Hi-C data is especially useful for assembling chromosome level sequences, or providing validation.
Gene editing (GE) technologies including CRISPR-cas9 allow us to precisely introduce changes to the genome. In its simplest form, GE is used to modify a position in order to disrupt a DNA sequence such as a promoter or gene. By doing so it may then be possible to detect the effect of the disruption through functional testing such as expression analysis, reporter gene activity, protein expression, cell morphology etc. In more complex designs it is possible to construct specific changes to a genome, from changing a single nucleotide base to adding an entire gene.
Related lab equipment:
|Microscope||Axio Vert.A1||Zeiss||Click here|
|Cell counter||TC20||Biorad||Click here|
|CO2-incubator||Model371||Thermo Scientific||Click here|
|Cooling Incubators||KT53/KT170||Binder||Click here|
|Biological safety cabinets||Mars 1200, Class2||Labogene||Click here|
|Biological safety cabinets||MSC 1.2 Advantage||Thermo Scientific||Click here|
|Real Time PCR Instrument||CFX96 Touch||Bio Rad||Click here|
For information regarding access to instruments and associated costs, please contact Matthew P. Kent or Kristil Sundsaasen.
Website updated: 26.06.2019