We are one of the five nodes of the HiLIFE Genome Analysis Infrastructure at the University of Helsinki, and offer the following genome profiling services at the Biomedicum Functional Genomics Unit (FuGU). Below you can find short description of our services. Complete information about ordering and contacts are found in FuGU web pages.
Targeted next-generation sequencing services: Services routinely provided by FuGU include targeted DNA sequencing (exome, ready-made and custom gene panels) using a number of different library preparations systems, such as HaloPlex, Agilent SureSelect, Illumina TruSeq systems, Roche SeqCap exome kits and Miseq or NextSeq500 instrumentation. Sequencing read length ranges from 36 to over 300 bases depending on the instrument. The service includes sample QC, library preparation, sequencing, data pre-processing and analysis if requested by the customer.
Transcriptome analysis: FuGU provides transcriptome analysis using Illumina sequencing instrumentation (MiSeq and NextSeq500). Gene expression profiling using Affymetrix and Agilent microarray systems is also possible. Transcriptome analysis includes nucleic acid QC, sample labelling, hybridization or sequencing and pre-processing of the data. Downstream data analysis is offered using a number of different options depending on the application.
Single-cell transcriptomics: We provide droplet-based single cell transcriptomics services in collaboration with Päivi Saavalainen’s group. This method uses barcoded microbeads utilizing a Drop-seq protocol developed in McCarroll lab at the Harvard Medical School (Macosko et al., Cell, 2015). A starting amount of 100,000 cells is required. For more information, see Single cell service lab.
Identity testing by ForenSeq: We provide genotyping services by MiSeq FGx™ Forensic Genomics System which is designed to detect more than 200 DNA markers in a single reaction. The markers have been designed for identity testing, estimation of ancestry, and population genetic analysis. Thus, the system is versatile and can be applied to track the mix-up of samples, such as cell lines or biopsies and formalin-fixed samples from pathology or service laboratories. The ForenSeq system is based on the detection of short tandem repeats and single-nucleotide polymorphisms specific for sex chromosomes, as well as e.g. hair and eye colour. The minimum amount of starting material is as low as 100 pg of DNA.
RT-qPCR by Fluidigm Biomark HD: FuGU has low and high-throughput options for RT-qPCR using Roche LightCycler 4800 and Fluidigm Biomark HD and NGS to e.g. validate the findings from whole transcriptome analyses. Roche LightCycler is cost-effective in small projects (up to 12 samples and 12 genes), whereas Fluidigm Biomark HD, where reactions are carried out in nanoliter volumes, becomes the cheapest and fastest option when the number of samples and genes is high.
Olink targeted biomarker protein analysis: This service has been set-up in 2015 and it is based on detecting specific protein expression by antibodies that are linked with oligos. Each protein is detected by two antibodies, which are linked with complementary oligos. Binding of the oligos can be detected and protein expression from up to 90 proteins from 92 samples is quantified using qPCR.
Nucleic acid QC and extraction: The QC analysis from thousands of different samples is carried out in FuGU each year. We have different instruments (Qubit, NanoDrop Agilent 2100 Bioanalyzer and TapeStation) for measuring the concentration, purity and size of nucleic acids depending on the application. We also provide RNA or DNA extraction from blood, cells or fresh frozen tissue sample. RNA and DNA can also be extracted from the same sample if requested by the customer.
Bioinformatics: We provide computational analyses for both next-generation sequencing and microarray data. The analysis services are categorized into basic and advanced data analysis according to the scope and objectives of the study. Detailed description can be found in FuGU web site.