NGS and Genomics Services

Biomedicum Functional Genomics Unit (FuGU) provides a wide range of Illumina next-generation sequencing (NGS), NanoString, microarray and qRT-PCR services both within and outside of Finland. Our focus is in transcriptomics services as well as services for targeted genomics covering exome sequencing and focused gene panels. Our services cover consultation in experiment design, sample QC, sample processing for NGS or microarrays, sequencing using Illumina technology (NextSeq 500 and MiSeq FGx) and computational data analysis.

For more details please contact fugu-support@helsinki.fi or please view our full range of services and prices from the HILIFE iLab online system.

FuGU can quantitate your RNA and DNA samples with our TapeStation 4200, Qubit and Victor Nivo instruments.

TapeStation 4200 analysis

Provides a fragment length analysis plot of your RNA, DNA and Genomic DNA samples. It also provides you with the concentration of your samples and a quality analysis score for RNA and Genomic DNA (RIN and DIN scores).

ScreenTape analysis available from FuGU Genomics: Quantitative range
High Sensitivity RNA ScreenTape 0.5 – 10 ng/ul
RNA ScreenTape 25 – 500 ng/ul
Genomic DNA ScreenTape 5 – 300 ng/ul
High Sensitivity D5000 (DNA) 0.01 – 1 ng/ul

We require a volume of 4-5 ul/sample (unused sample can be returned). If you have multiple samples please deliver in 8-strip or 96-well PCR plate format. In 96-well PCR plates, please pipette your samples in the order A1, B1, C1 etc.

Qubit analysis 

Fluorometric quantification of DNA or RNA Quantitation Range
RNA analysis 5-100 ng
DNA analysis 0.2-100 ng

Price depends upon number of sample. For large scale projects we would use Victor Nivo platereader to perform Qubit analysis (€2.75/sample (12-47 samples) or €1.99/sample for 48 samples or greater)

We require a volume of 4-5 ul/sample (unused sample can be returned). If you have multiple samples please deliver in 8-strip or 96-well PCR plate format. In 96-well PCR plates, please pipette your samples in the order A1, B1, C1 etc.

Please submit your service request from the HILIFE iLab online system. You can also contact us by sending an email to FuGU Support (fugu-support@helsinki.fi).

NextSeq 500 can operate in Mid Output mode (130M sequencing clusters) and High Output mode (400M sequencing clusters).

The NextSeq can offer flexible read lengths including, but not exclusive to: 2x40bp (High Output), 1x75bp (High Output), 2x75bp (Mid and High Output) and 2x150bp (Mid and High Output).

MiSeq FGx can operate in research mode and can generate between 1M to 25M sequencing clusters per run and can offer up to 2 x 300 bp reads with MiSeq V3 600 cycle flow cell.

All Sequencing Services include

  • Sequencing library quality control (Agilent TapeStation, Qubit)
  • Sequencing
  • Data pre-processing (fastq conversion)

Library pool requirements

  • Illumina compatible sequencing library
  • Concentration more than 5 nM (calculated based on qPCR analysis OR based on Qubit concentration and average fragment size)
  • Volume of at least 20 ul

Please submit your service request from the HILIFE iLab online system, or you can also contact us by sending an email to FuGU Support (fugu-support@helsinki.fi).

 

FuGU provides whole genome, exome, and targeted sequencing (ready-made and custom gene panels). Sequencing read length ranges from 50 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. 

For more details please contact fugu-support@helsinki.fi or please view our full range of services and prices from the HILIFE iLab online system.

 

FuGU has several options for RNA-seq sample preparation including:

  • A “Bulkseq” 3’UTR counting gene expression profiling method based broadly on BRBseq/Dropseq which can be used to generate data for multiple samples at ultra-low cost
  • Coding transcriptome (mRNA capture)
  • Whole transcriptome sequencing (ribodepletion)
  • Small RNA/miRNA sequencing

We can also provide Bioinformatics support for all transcriptomics projects.

Please submit your service request from the HILIFE iLab online system.

 

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. 

Please submit your service request from the HILIFE iLab online system.

 

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. 

Please submit your service request from the HILIFE iLab online system.

 

NanoString nCounter targeted assays can be applied for mRNA, miRNA and protein expression, SNV, CNV and gene fusion analyses. The technology is based on direct hybridization of target-specific color-coded probes and therefore, no cDNA synthesis or amplification of RNA/DNA is required. Starting material can originate from FFPE samples, tissue, cells, or plasma.

Standard gene expression panel contains up to 770 genes and is customizable up to 30 additional unique targets. The NanoString assays include panels for e.g. oncology, immunology and neurology. For further inquiries, please contact FuGU Support.

Please submit your service request from the HILIFE iLab online system.

 

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.

High-throughput qPCR

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.

For further inquiries, please contact FuGU Support.

Please submit your service request from the HILIFE iLab online system.

 

The Agilent SureScan Dx Microarray Scanner is CE-marked and is thus suitable to scan diagnostic slides. The compatible dyes include Cyanine 3, Cyanine 5, as well as Alexa 647, 555, and 660. The SureScan Dx Microarray Scanner has dynamic autofocus and a resolution range of 2, 3, 5 and 10 um. Scanning non-mirrored slides with low intrinsic fluorescence is possible. 

Please submit your service request from the HILIFE iLab online system.

 

FuGU offers a full sample QC, probe preparation, hybridization and scanning service for Agilent CGH and Gene Expression Microarrays.

Service includes

  • Sample quality control (Agilent TapeStation, Qubit)
  • Probe preparation, quantitation and quality control (Agilent TapeStation, Qubit)
  • Hybridization of probes to arrays
  • Scanning of arrays with Agilent SureScan Dx

For more details please contact fugu-support@helsinki.fi, or submit your service request from the HILIFE iLab online system.