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OMICS Genomics

About us

CF OMICS-Genomics provides a broad array instrumentation and services, including Sanger sequencing of plasmid and PCR products on the Life Technologies ABI 3500 capillary array sequencing platform, fragment analysis (Amplified Fragment Length Polymorphism mapping, microsatellite STR analysis, SNP genotyping) on the same platform and Next Generation Sequencing on the Illumina MiSeq platform.

The Facility also offers the microarray platforms and a battery of DNA/RNA quality control tests for use by individual customers.

Keywords

  • Next Generation Sequencing
  • Sanger Sequencing
  • DNA/RNA quality control
  • DNA/RNA quantity control
  • MiSeq Illumina

Team and contacts

Hrda
  • RNDr. Štěpánka Hrdá

  • Head of Genomics team
  • +420 325 873 935
  • +420 325 873 936
Místnost M1.012; J1.016
Místnost
M1.012; J1.016

Equipment


  • Agilent 2100 Bioanalyzer

    This instrument provides a complete solution for DNA/RNA quality control of limiting amounts of sample on the chips. The micro-capillary electrophoresis-based technology provides high quality digital reporting of size range and quantity on a single platform. Bioanalyzer system has the resolution and power to quantify a few picograms with as little as a couple microliters of samples. Several kits are available at CF.

  • Nanodrop 2000 UV-Vis spectrophotometer

    The spectrophotometer is used to measure microvolumes (0.5 – 2 µL) of nucleic acid and protein samples. No dilutions required, even for highly concentrated samples. Patented sample retention system automatically optimizes pathlength to accommodate low and high concentrations . Calculates sample purity ratios (260/280 nm and 260/230 nm). Recommended for Sanger Sequencing.

  • MiSeq Illumina

    This high-throughput massive parallel sequencer allows to access more focused applications such as targeted gene sequencing, RNA-Seq, metagenomics, small genome sequencing, amplicon sequencing and others. New MiSeq reagents enable up to 15 Gb of output with 25 M sequencing reads and 2 x 300 bp read lengths.

  • 3500 Genetic Analyzer Applied Biosystems

    This sequencer is fluorescence based DNA analysis instrument using capillary electrophoresis technology with 24 capillaries. Analyzer is fully automated, from sample loading to primary data analysis, for DNA sequencing and fragment analysis.

  • Covaris M220

    This focused ultrasonicator is designed for Next-Gen Sequencing applications requiring fragment sizes between 150bp and 5kb. It is used to mechanically shear nucleic acids into smaller fragments by focused ultrasonic waves and is a recommended instrument to mechanically shear nucleic acids in Illumina protocols. MicroTUBE (50ul)  and miniTUBE (130 ul) are available at CF.

  • Quantus Fluorometer

    The fluorometer quantitates DNA, RNA, and protein with high accuracy, sensitivity and simplicity. Fluorescence-based nucleic acid quantification methods are more sensitive than absorbance-based methods, allowing you to quantitate low-level DNA samples accurately. Recommended for Next-Gen Sequencing.  Several kits are available at CF.

  • Axon GenePix 4000B Microarray Scanner

    This confocal laser scanner is used to analyze standard two-color (Cy3 and Cy5) microarrays. GenePix software allows for adjustable scan area and resolution, as well as automated spot finding. The Genepix 4000B scans at resolutions between 5 and 100 microns.

  • LightCycler 480 Real-TimePCR, Roche

  • M220 Focused-ultrasonicator™, Covaris

Our Services

Sanger sequencing

  • Single read sequencing service for plasmids and PCR fragments
  • Results typically in 1-2 working days
  • Typical length of read min. 800 bp
  • Troubleshooting support

Sample preparation details and sample sheet

 

 

 

Fragment analysis

  • Amplified Fragment Length Polymorphism (AFLP) mapping
  • Microsatellite STR Analysis
  • SNP Genotyping

 

 

Next Generation Sequencing

  • DNA and RNA applications
  • Raw data is provided to the customer as the Facility does not provide data analysis services.

 

 

Quality and quantity control of nucleic acids

  • Quantity control of nucleic acids with a spectrophotometer Nanodrop 2000
  • Quantity control of nucleic acids with a fluorometer Quantus
  • Quality control of nucleic acids with a Bioanalyzer 2100 (Agilent)

References and Publications

POTENTIAL FOR COOPERATION

More than 12 years’ experience in capillary sequencing – more than 35 000 samples per year. Single read sequencing service for plasmids and PCR fragments. Fragment analysis (Amplified Fragment Length Polymorphism (AFLP) Mapping, Microsatellite STR Analysis, SNP Genotyping).

  • High-throughput massive parallel sequencing on MiSeq – Illumina (RNA-Seq, De novo sequencing, Targeted resequencing). Library preparation.
  • Access to other equipment – Agilent 2100 Bioanalyser, Covaris M220.