FuGU Genomics Instruments

FuGU's Illumina NextSeq 500 sequencer can be be used for medium scale Next Generation Sequencing (NGS) projects including:

  • Whole transcriptome RNAseq (after ribo-depletion)
  • Coding transcriptome RNAseq (after mRNA capture with PolyA binding beads
  • Exome-seq
  • Whole genome sequencing for bacterial and small genomes 
  • MethylSeq
  • Shotgun Metagenomics

The NextSeq 500 is frequently used by laboratories which make there own sequencing libraries but need access to a medium-scale sequencer.

For larger scale sequencing projects, sequening libraries can be made at FuGU and then sequenced on the NovaSeq 6000 sequencer which is located at FIMM which is one of our HGI partner labs.

FuGU's Illumina MiSeq FGx can be used for both normal Illumina sequencing projects and for Verogen's forensic "Forenseq" sequencing for human identity testing. The sequencer is also availabe for use for research labs outside of FuGU. 

Total reads from a MiSeq run range from 1M (Nano) to 25M (V3). The MiSeq V3 600 cycle flow cell can produce up to 2x300bp reads.

Examples of projects run at FuGU:

"Research mode":

  • 16S rRNA amplicon metagenomics
  • Amplicon-seq
  • Whole genome sequencing of small bacterial and fungal genomes
  • Sequencing of small exome panels

"Forensics mode":

  • ForenSeq DNA Signature Prep
  • ForenSeq mtDNA Control region (on request)
  • ForenSeq mtDNA Whole genome (future)

The NanoString nCounter SPRINT Profiler uses NanoString’s molecular barcoding technology to profile RNA, DNA or protein samples.

Features:

  • Fast turnaround (potentially within 1 day)
  • Samples can be directly quantitated without an intermediate PCR step
  • Multi-analyte assays can assay both RNA and Protein from the same sample
  • Panels available include:
    • Oncology
    • Immunology
    • Neuroscience

For more information please contact FuGU support at fugu-support@helsinki.fi

NanoString's website

 

High-throughput qPCR using Fluidigm's 48.48 and 96.96 array format

  • Suitable for both TaqMan and EvaGreen chemistry
  • 48.48 array - 48 samples and 48 assays gives 2304 total data points per qPCR run
  • 96.96 array - 96 samples and 96 assays gives 9216 total data points per qPCR run
  • The Biomark can also be used for detecting protein Biomarkers from Biological samples using Olink technology (Olink Target 96)

Each Olink Target 96 panel can process 90 Biological samples at a time using the Proximity Extension Assay (PEA) technique. Commonly used sample types include blood serum and plasma

Full list of panels and sample types supported can be found on the Olink webpage at:

https://www.olink.com/products/

Agilent TapeStation 4200 provides high-throughput fragment analysis of RNA, DNA and Genomic DNA

ScreenTapes commonly used at FuGU:

  • RNA ScreenTape - (25-500 ng per microlitre)
  • RNA HighSensitivity - (0.5-25 ng per microlitre)
  • DNA D5000 High Sensitivity (0.01 - 1 ng per microlitre)
  • Genomic DNA (5-300 ng per microlitre) 

 

 

 

  • Agilent 2100 Bioanalyzer
  • Victor Nivo Platereader
  • Qubit Fluorometer
  • Thermo Nanodrop
  • Covaris S2 Sonicator
  • Three PCR machines (Bio-Rad T100, S1000 and Finnzyme DNA Engine)