"High Throughput (DNA/RNA) Sequencing (HTS)" services
GCF has Illumina HiSeq4000, HiSeq2500 and NS500 sequencing instruments that can be used for a broad range of applications, including but not limited to:
- Whole genome sequencing
- Exome sequencing
- Protein-DNA/RNA interactions (ChIP-Seq, etc.)
- Small RNA discovery/expression
- Transcriptome sequencing for SNP detection, expression analysis, and splice variant detection
- Targeted resequencing
As there are many types of applications, so it is essential that you speak with us regarding the specific goals and technical aspects of your research projects. We can perform both single-end and paired-end sequencing up to 150 bp read lengths. Pricing is application specific and dependent on several factors e.g. choise of library preparation application, coverage (dependetn on number of reds per samples per lane), run base length and choice of single- or paired end read method of sequencing. Details about the HiSeq4000/2500 and NS500 systems can be found here.
Please contact us to discuss your project and how HTS sequencing can help you in your research.
"RNA in data out" microarray services
Our RNA in data out gene expression analysis services include a variety of assays. All whole genome expression analyses are offered as a full service. Users only need to provide us with total RNA samples. We will check the sample quantity and quality with QBit, NanoDrop, Agilent BioAnalyzer, amplify and label the samples, set up hybridization, process and scan the arrays, transfer data to users and include basic data analysis. Our bioinformaticians can also offer extended bioinformatics analysis as an optional service (for details see the bioinformatics service section). We currently offer:
- Whole genome expression analysis based on Illumina BeadArrays for human samples
Details about assys offered, can be found at Illumina web pages.
"DNA in data out" microarray services
DNA analysis applications available at GCF include SNP genotyping (GWAS), gene copy number (CNV) and DNA methylation analysis. Whole-genome genotyping arrays have become an invaluable tool for discovering variants that contribute to e.g. human diseases and phenotypes. The two primary applications of this technology, genome-wide association studies (GWAS) and copy number variant (CNV) analysis, have helped researchers begin to unravel the complex genetic architecture behind several diseases. Which platform to select mostly depends on the number of SNPs that you are interested in genotyping. However, most of the applications we currently offer are related to the Illumina platform. Currently we offer:
- Whole genome SNP genotyping and CNV analysis based on Illumina BeadArrays
- Illumina Focused and Custom SNP Panels (individual to 1536-plex)
- Illumina genome wide DNA methylation analysis
Detailed information about DNA analysis applications, can be found through Illumina web pages.
RNA/DNA Sample Preparation and Quality Control
High DNA/RNA quality is essential to obtain good data. Please se our general guidelines for sample preparation and DNA/RNA quality control.
The bioinformatics staff at Genomics Core Facility (GCF) focuses on helping customers design experiments to get maximum information out of the genomics experiments. We also provide assistance in statistical analysis and accessing biological background knowledge about genes and proteins.
One of the major headaches for genomics technology users is the data analysis. Previously a lot of focus was put on image analysis and normalisation to get the best possible data to work with, but with improved technology the focus has moved to how to derive biological understanding from the tidal wave of data that is produced. The process starts before any lab work is done, with a discussion on the experimental design. This is to evaluate the statistical power of the experiment and give input on randomization in the laboratory so that no unnecessary bias is introduced in the experiment. When the lab work is done, the data is pretreated and formatted according to current standards and/or fitted to customer need. Bioinformatics results, such as identifying differentially expressed genes or sample classifications, is routinely reported. Further work may involve determining which processes or pathways are most affected by the changes. We also have extensive experience in approaches to relate more complex datasets where gene expression is just a part of the experimental approaches and there is a need to integrate data. We prefer being involved in the planning of studies as early as possible so the sooner you contact us the better.
In brief, GRC offers relevant bioinformatics service related to all wet lab applications offered. This includes:
- Consultation on experimental design
- Quality control
- Data formatting and statistical summary
- Basic bioinformatics analysis