Biomedicum Functional Genomics Unit (FuGU)

 

Overview of the Services


We are one of the five nodes of the HiLIFE Genome Analysis Infrastructure (HGI) at the University of Helsinki, and offer the following genome profiling services: 

Next-generation sequencing services: Services provided by FuGU include whole genome, exome, and targeted sequencing (ready-made and custom gene panels). 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 has several options for RNA-seq sample preparation (mRNA capture, whole transcriptome sequencing, small RNA/miRNA sequencing). Gene expression profiling using Agilent microarray systems is also possible. Transcriptome analysis includes nucleic acid QC, sample labelling, hybridization or sequencing and pre-processing of the data.

Identity testing by ForenSeq: Genotyping service is provided 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. The system 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 provides both the EvaGreen and TaqMan based RT-qPCR and digital PCR assays for Fluidigm Biomark HD where reactions are carried out in nanoliter volumes.

Olink targeted biomarker protein analysis: This service 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: We use Qubit, Agilent TapeStation and Victor Nivo plate reader 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.

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.

 

Contacts

FuGU Support: fugu-support@helsinki.fi







 

 

Location and hours of operation

Hours Location

Monday - Friday

8:00h - 16:00h    

Room C504a/b

Biomedicum Helsinki 1

Haartmaninkatu 8

00290 Helsinki, Finland

Links and Resources

  1. Biomedicum Functional Genomics Unit (FuGU) web site
  2. HILIFE HGI Biomedicum Functional Genomics Unit web page

Contacts

Name Role Phone Email Location
Martyn James
Lab Coordinator
 
+358-50-4420228
 
fugu-support@helsinki.fi
 

 
Taru Jämbäck
NGS Service Expert
 
+358-50-4420228
 
fugu-support@helsinki.fi
 

 
Hanna Pesonen
NGS Service Expert
 
+358-50-4420228
 
fugu-support@helsinki.fi
 

 
Juho Väänänen
Bioinformatician
 
+358-50-4420228
 
fugu-support@helsinki.fi
 

 
Outi Monni
Director
 
+358-50-4160736
 
outi.monni@helsinki.fi
 

 

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