OMICS Genomics

OMICS Genomics

RNDr. Štěpánka Hrdá

RNDr. Štěpánka Hrdá — Laboratory head

The Faculty of Science of the Charles University

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.

 

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.

News

Services

We offer Sanger sequencing, Fragment analysis, Next Generation Sequencing and Quality and quantity control of nucleic acids.

Services

01

Sanger sequencing
02

Fragmentační analýza DNA
03

Next Generation Sequencing

Equipment

Our Equipment

Bioanalyzér 2100, Agilent

Bioanalyzér 2100, Agilent

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

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

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, Life Technologies

3500 Genetic Analyzer, Life Technologies

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.

Fluorometr Quantus, Promega

Fluorometr Quantus, Promega

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.

Covaris M220

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.

Axon GenePix 4000B Microarray Scanner

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.

Publications

2017

Bhattacharyya T, Gregorova S, Mihola O, Anger M, Sebestova J, Denny P, Simecek P, Forejt J.: Mechanistic basis of infertility of mouse intersubspecific hybrids. Proc Natl Acad Sci U S A. 2013 Jan 17.

Youngson N.A., Epp T., Roberts A.R., Daxinger L., Ashe A., Huang E., Lester K.L., Harten S., Kay G.F., Cox T., Matthews J.M., Chong S. and Whitelaw E.: No evidence for cumulative effects in a Dnmt3b hypomorph across multiple generations. 2013. Mammalian Genome.

Laššuthová P, Gregor M, Sarnová L, Machalová E, Sedláček R, Seeman P: Clinical, In Silico, and Experimental Evidence for Pathogenicity of Two Novel Splice Site Mutations in the SH3TC2 Gene. J Neurogenet 2012 26(3-4): 413-20. [pubmed] [doi]

2016

Kasparek P, Krenek P, Buryova H, Suchanova S, Beck IM, Sedlacek R: Transgenic mouse model expressing tdTomato under involucrin promoter as a tool for analysis of epidermal differentiation and wound healing. Transgenic Res 201221(3): 683-9. [pubmed] [doi]

Fafilek B, Krausova M, Vojtechova M, Pospichalova V, Tumova L, Sloncova E, Huranova M, Stancikova J, Hlavata A, Svec J,Sedlacek R, Luksan O, Oliverius M, Voska L, Jirsa M, Paces J, Kolar M, Krivjanska M, Klimesova K, Tlaskalova-Hogenova H,Korinek V: Troy, a Tumor Necrosis Factor Receptor Family Member, Interacts With Lgr5 to Inhibit Wnt Signaling in Intestinal Stem Cells. Gastroenterology 2012. [pubmed] [doi]

Jirouskova M, Zbodakova O, Gregor M, Chalupsky K, Sarnova L, Hajduch M, Ehrmann J, Jirkovska M, Sedlacek R: Hepatoprotective Effect of MMP-19 Deficiency in a Mouse Model of Chronic Liver Fibrosis. PLoS One 2012 7(10): e46271. [pubmed] [doi]