Core Facility Genomics

Main Activity

The Core Facility offers services and access to the instrument for genomic analyses. Equipment for massively parallel (Next Generation) sequencing, DNA microarrays as well as capillary sequencing and real-time qPCR (including high-throughput and digital PCR) is available or will be available soon. Services: Nextera and TruSeq compatible NGS library preparation including precise small samples, capillary sequencing, gene expression microarrays, CGH and cytogenetics microarrays.

Unique Features

Combination of high-end equipment and expertise for the complete experimental workflow from advanced sample preparation to complex genome analysis. Precise sample preparation techniques (cell sorting, microdissection) followed by combination of various complementary approaches in the analysis of the genome (massive parallel sequencing, microarrays, quantitative PCR) will make it possible to perform even very complex experimental designs including single cell genomics or diseased vs. healthy cells genome and transcriptome analyses.

Key Equipment (Core Facility fully operational from 2014)

• High-throughput massive parallel sequencers
  • Illumina MiSeq
  • Roche GS Junior
  • whole-genome NG sequencer (end 2014)
• Cell analysis system
  • Olympus Scan^R
• Microarray system
  • Agilent SureScan
• qPCR
  • Roche LC480
  • HT and digital PCR system (end 2014)

All CEITEC core facilities are available to external users (academia and companies). Czech and international researchers from universities and research institutes interested in accessing core facilities can benefit from support of research infrastructure NCLG, funded by the Ministry of Education, Youth and Sports of the Czech Republic.

list / cards

Name and position	E-mail	Phone
Tereza Cermanová Specialist		+420 54949 7934
Jana Jedličková laborantka		+420 54949 6997
Andrea Ondrůjová odborná pracovnice
Karol Pál PhD student		+420 54949 6926
Lukáš Tichý, Ph.D. PhD student		+420 532 234 626
Nina Dvořáčková odborná asistentka
Zuzana Vrzalová PhD student
Boris Tichý, Ph.D. Research Group Leader		+420 54949 8317, +420 733 141 527
Filip Pardy Specialist		+420 54949 8630
Kamila Réblová, Ph.D. Researcher		+420 54949 7586, +420 532 234 625
Jiří Štika odborný pracovník ve výzkumu
Larissa Wartha

SELECTED PUBLICATIONS

2017

• BENCUROVA, P; BALOUN, J; MUSILOVA, K; RADOVA, L; TICHY, B; PAIL, M; ZEMAN, M; BRICHTOVA, E; HERMANOVA, M; POSPISILOVA, S; MRAZ, M; BRAZDIL, M, 2017:MicroRNA and mesial temporal lobe epilepsy with hippocampal sclerosis: Whole miRNome profiling of human hippocampus. EPILEPSIA 58 (10), p. 1782 - 1793.
• PAL, K; BYSTRY, V; REIGL, T; DEMKO, M; KREJCI, A; TOULOUMENIDOU, T; STALIKA, E; TICHY, B; GHIA, P; STAMATOPOULOS, K; POSPISILOVA, S; MALCIKOVA, J; DARZENTAS, N, 2017:GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data. BIOINFORMATICS 33 (23), p. 3802 - 3804.

2016

• KUBESOVA, B; PAVLOVA, S; MALCIKOVA, J; KABATHOVA, J; RADOVA, L; TOM, N; TICHY, B; PLEVOVA, K; KANTOROVA, B; FIEDOROVA, K; KISSOVA, J; GISSLINGER, B; GISSLINGER, H; MAYER, J; KRALOVICS, R; POSPISILOVA, S; DOUBEK, M, 2016:Low-Burden TP53 Mutations Occur in Chronic Phase of Myeloproliferative Neoplasms Regardless of Hydroxyurea Administration, Disease Type, and JAK2 Status. BLOOD 128 (22)

2015

• BRAZDILOVA, K; PLEVOVA, K; FRANCOVA, HS; KOCKOVA, H; CHMELIKOVA, M; BORSKY, M; BURCKOVA, K; KANTOROVA, B; TICHY, B; SKABRAHOVA, H; BRYCHTOVA, Y; MAYER, J; DOUBEK, M; POSPISILOVA, S, 2015:Single Cell Analysis of IG Genes in CLL: Cases with Multiple IGH Rearrangements Are Constituted of Several Independent Clones Even When Indistinguishable By Flow Cytometry. BLOOD 126 (23)
• MALCIKOVA, J; STANO-KOZUBIK, K; TICHY, B; KANTOROVA, B; PAVLOVA, S; TOM, N; RADOVA, L; SMARDOVA, J; PARDY, F; DOUBEK, M; BRYCHTOVA, Y; MRAZ, M; PLEVOVA, K; DIVISKOVA, E; OLTOVA, A; MAYER, J; POSPISILOVA, S; TRBUSEK, M, 2015:Detailed analysis of therapy-driven clonal evolution of TP53 mutations in chronic lymphocytic leukemia. LEUKEMIA 29 (4), p. 877 - 885.
• TOM, N; MALCIKOVA, J; RADOVA, L; KANTOROVA, B; PARDY, F; PAVLOVA, S; PAL, K; MRAZ, M; TICHY, B; DOUBEK, M; BRYCHTOVA, Y; PLEVOVA, K; MAYER, J; TRBUSEK, M; POSPISILOVA, S, 2015:MUTATIONS IN THE TP53 GENE SHOW FEATURES OF SOMATIC HYPERMUTATION PROCESS WITH PROMINENT DIFFERENCE BETWEEN IGHV MUTATED AND UNMUTATED CHRONIC LYMPHOCYTIC LEUKEMIA. HAEMATOLOGICA 100 , p. 224 - 225.

2013

• KAUCKA, M; PLEVOVA, K; PAVLOVA, S; JANOVSKA, P; MISHRA, A; VERNER, J; PROCHAZKOVA, J; KREJCI, P; KOTASKOVA, J; OVESNA, P; TICHY, B; BRYCHTOVA, Y; DOUBEK, M; KOZUBIK, A; MAYER, J; POSPISILOVA, S; BRYJA, V, 2013:The Planar Cell Polarity Pathway Drives Pathogenesis of Chronic Lymphocytic Leukemia by the Regulation of B-Lymphocyte Migration. CANCER RESEARCH 73 (5), p. 1491 - 1501.
• KHARE, V; LYAKHOVICH, A; DAMMANN, K; LANG, M; BORGMANN, M; TICHY, B; POSPISILOVA, S; LUCIANI, G; CAMPREGHER, C; EVSTATIEV, R; PFLUEGER, M; HUNDSBERGER, H; GASCHE, C, 2013:Mesalamine modulates intercellular adhesion through inhibition of p-21 activated kinase-1. BIOCHEMICAL PHARMACOLOGY 85 (2), p. 234 - 244.
• KREJCI, M; DOUBEK, M; BRYCHTOVA, Y; STEHLIKOVA, O; CHOVANCOVA, J; TICHY, B; FRANCOVA, HS; NAVRATIL, M; TOMISKA, M; HORKY, O; POSPISILOVA, S; MAYER, J, 2013:Fludarabine with cytarabine followed by reduced-intensity conditioning and allogeneic hematopoietic stem cell transplantation in patients with poor-risk chronic lymphocytic leukemia. ANNALS OF HEMATOLOGY 92 (2), p. 249 - 254.

2012

• AGATHANGELIDIS, A; DARZENTAS, N; HADZIDIMITRIOU, A; BROCHET, X; MURRAY, F; YAN, XJ; DAVIS, Z; VAN GASTEL-MOL, EJ; TRESOLDI, C; CHU, CC; CAHILL, N; GIUDICELLI, V; TICHY, B; PEDERSEN, LB; FORONI, L; BONELLO, L; JANUS, A; SMEDBY, K; ANAGNOSTOPOULOS, A; MERLE, 2012:Stereotyped B-cell receptors in one-third of chronic lymphocytic leukemia: a molecular classification with implications for targeted therapies. BLOOD 119 (19), p. 4467 - 4475.
• JANIKOVA, A; MARECKOVA, A; DVORAKOVA, D; BORTLICEK, Z; TICHY, B; NAVRATIL, M; KRAL, Z; POSPISILOVA, S; MAYER, J, 2012:A real-time (PCR) for a real life ...? Quantitative evaluation of BCL2/IGH in follicular lymphoma and its implications for clinical practice. EXPERIMENTAL HEMATOLOGY 40 (7), p. 528 - 539.
• KOSTARELI, E; GOUNARI, M; JANUS, A; MURRAY, F; BROCHET, X; GIUDICELLI, V; POSPISILOVA, S; OSCIER, D; FORONI, L; DI CELLE, PF; TICHY, B; PEDERSEN, LB; JURLANDER, J; PONZONI, M; KOUVATSI, A; ANAGNOSTOPOULOS, A; THOMPSON, K; DARZENTAS, N; LEFRANC, MP; BELESS, 2012:Antigen receptor stereotypy across B-cell lymphoproliferations: the case of IGHV4-59/IGKV3-20 receptors with rheumatoid factor activity. LEUKEMIA 26 (5), p. 1127 - 1131.
• KOZUBIK, KS; MALCIKOVA, J; TRBUSEK, M; TOM, N; DOUBEK, M; BRYCHTOVA, Y; SMARDOVA, J; MAYER, J; POSPISILOVA, S; TICHY, B, 2012:Clonal Selection of TP53 Mutations in Chronic Lymphocytic Leukaemia Detected by Ultra-deep Pyrosequencing. EUROPEAN JOURNAL OF CANCER 48 , p. S146 - S146.
• MRAZ, M; DOLEZALOVA, D; PLEVOVA, K; KOZUBIK, KS; MAYEROVA, V; CERNA, K; MUSILOVA, K; TICHY, B; PAVLOVA, S; BORSKY, M; VERNER, J; DOUBEK, M; BRYCHTOVA, Y; TRBUSEK, M; HAMPL, A; MAYER, J; POSPISILOVA, S, 2012:MicroRNA-650 expression is influenced by immunoglobulin gene rearrangement and affects the biology of chronic lymphocytic leukemia. BLOOD 119 (9), p. 2110 - 2113.

2011

• JANIKOVA, A; TICHY, B; SUPIKOVA, J; STANO-KOZUBIK, K; POSPISILOVA, S; KREN, L; VASOVA, I; SALEK, D; MAYER, J, 2011:Gene expression profiling in follicular lymphoma and its implication for clinical practice. LEUKEMIA & LYMPHOMA 52 (1), p. 59 - 68.

2010

• KOTASKOVA, JANA; TICHY, BORIS; TRBUSEK, MARTIN; FRANCOVA, HANA SKUHROVA; KABATHOVA, JITKA; MALCIKOVA, JITKA; DOUBEK, MICHAEL; BRYCHTOVA, YVONA; MAYER, JIRI; POSPISILOVA, SARKA, 2010:High Expression of Lymphocyte-Activation Gene 3 (LAG3) in Chronic Lymphocytic Leukemia Cells Is Associated with Unmutated lmmunoglobulin Variable Heavy Chain Region (IGHV) Gene and Reduced Treatment-Free Survival. JOURNAL OF MOLECULAR DIAGNOSTICS 12 (3), p. 328 - 334.
• MALCIKOVA, J; TICHY, B; DAMBORSKY, J; KABATHOVA, J; TRBUSEK, M; MAYER, J; POSPISILOVA, S, 2010:Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation. BIOLOGICAL CHEMISTRY 391 (2 III), p. 197 - 205.

PROJECTS

• NCLG - Natioonal Center for Medical Genomic (LM2015091), MEYS, 2016 - 2019
• NCLG - Národní centrum lékařské genomiky - modernizace infrastruktury a výzkum genetické variability populace (CZ.02.1.01/0.0/0.0/16_013/0001634), MEYS, 2017 - 2019
• RIAT-CZ (ATCZ40), Interreg CZ-AT, 2016 - 2018

Filter

Filtr Search Research group / CF — select — Functional Properties of Nanostructures - Josef HumlíčekSmart Nanodevices - Jaromír HubálekExperimental Biophotonics - Radim ChmelíkFabrication and Characterisation of Nanostructures - Tomáš ŠikolaDevelopment of Methods for Analysis and Measuring - Petr KlapetekMaterials Characterization and Advanced Coatings - Jozef KaiserPlasma Technologies - Lenka ZajíčkováSynthesis and Analysis of Nanostructures - Jiří PinkasMultiscale Modelling and Measurements of Physical Properties - Roman GrögerAdvanced Ceramic Materials - Martin TrunecCybernetics in Material Science - Pavel VáclavekAdvanced Polymers and Composites - Josef JančářAdvanced Metallic Materials and Metal Based CompositesGlycobiochemistry - Michaela WimmerováMolecular Microbiology - Alois ČížekZoonoses - Břetislav KoudelaOrthopaedics and Surgery - Pavel ProksAnimal Immunogenomics - Petr HořínAnimal Cytogenomics - Jiří RubešMammalian Reproduction - Martin AngerBehavioural and Social Neuroscience - Milan BrázdilApplied Neuroscience - Irena RektorováMedical Genomics - Šárka PospíšilováMolecular Oncology - Solid Cancer - Ondřej SlabýInherited Diseases - Transtricptional Regulation - Dalibor BlažekAdaptive Immunity Group - Dmitriy ChudakovBioanalytical Instrumentation - František ForetPlant Cytogenomics - Martin LysákFunctional Genomics and Proteomics of Plants - Jan HejátkoHormonal Crosstalk in Plant Development - Helene Robert BoisivonProteomics - Zbyněk ZdráhalDevelopmental and Cell Biology of Plants - Tomasz NodzynskiChromatin Molecular Complexes - Jiří FajkusDevelopmental and Production Biology – Omics Approaches - Břetislav BrzobohatýPlant Stress Signalling and Adaption - Vanesa Beatriz TognettiPlant Molecular Biology - Karel ŘíhaRNA Quality Control - Štěpánka VaňáčováNanobiotechnology - Petr SkládalRNA based regulation of Gene Expression - Peter LukavskyStructural Biology of Gene Regulation - Richard ŠteflStructural Virology - Pavel PlevkaStructure and Dynamics of Nucleic Acids - Jiří ŠponerStructure and Interaction of Biomolecules at Surfaces - Miroslav FojtaComputational Chemistry - Jaroslav KočaMulti-modal and Functional Neuroimaging - Ivan RektorCF: Core Facility GenomicsCF: Core Facility X-Ray Diffraction and Bio-SAXSCF: CEITEC NanoCF: Josef Dadok National NMR CentreCF: Core Facility Biomolecular Interaction and CrystalizationCF: Core Facility Cryo-Electron Microscopy and TomographyCF: Core Facility ProteomicsCF: Multimodal and Functional Imaging LaboratoryCF: Core Facility NanobiotechnologyStrucure of Biosystems and Molecular Materials - Radek MarekNon-Coding Genome - Lukáš TrantírekProtein Structure and Dynamics - Lukáš ŽídekProtein-DNA Interactions - Konstantinos TripsianesERA Chair - RNA and Immunity - Mary O'ConnellMicroenvironment of Immune Cells - Marek MrázCF: Cellular ImagingCF: Plant Sciences Core FacilityFunctional Genomics - Michal ŠmídaInteraction Protein-Protein and Protein-Membrane - Robert VáchaMagneto-Optical and THz Spectroscopy - Petr NeugebauerMolecular Nanostructures at Surfaces - Jan ČechalNanomagnetism and spintronics - Vojtěch Uhlíř Institution — select — CEITEC HeadquartersCEITEC Masaryk UniversityCEITEC Brno University of TechnologyCEITEC Mendel University in BrnoCEITEC University of Veterinary and Pharmaceutical Sciences BrnoCEITEC Institute of Physics of Materials, Academy of Science CZCEITEC Veterinary Research Institute Technology — select — Nanolitography infrastructureChemical & Thermal processesEtching & DepositionPackaging & TestingElectrical & Magnetic measurementsOptical measurementsProbe microscopy & NanomanipulationIn situ fabrication & CharacterizationLiquid ChromatographyElectrophoresisX-ray DiffractionX-ray ScatteringBiomolecular Interactions and characterizationBiomolecular crystallizationConfocal microscopyWidefield microscopyConfocal microscopy for live cell imagingPhytotronsSmall-size growth chambersGreenhouse

Equipment	Research group / CF	Profile card
Agilent Tapestation	CF: Core Facility Genomics
Capillary sequencer ABI3500	CF: Core Facility Genomics
DNA microarray scanner	CF: Core Facility Genomics
Droplet digital PCR BioRad QX200	CF: Core Facility Genomics
FACS cell sorter BD Aria Fusion	CF: Core Facility Genomics
Flow cytometer FACS Verse	CF: Core Facility Genomics
Fluidigm C1 single-cell system	CF: Core Facility Genomics
Illumina MiSeq	CF: Core Facility Genomics
Illumina MiSeq	CF: Core Facility Genomics
Illumina NextSeq 500	CF: Core Facility Genomics
Illumina NextSeq 500	CF: Core Facility Genomics
Liquid handling robot Tecan	CF: Core Facility Genomics
Olympus ScanR inverted fluorescent microscope	CF: Core Facility Genomics
qPCR QuantStudio 12k	CF: Core Facility Genomics
qPCR QuantStudio 12k	CF: Core Facility Genomics
Real-time PCR LightCycler 480	CF: Core Facility Genomics
Real-time PCR LightCycler 480	CF: Core Facility Genomics

Equipment	Partner
Fragment Analyzer, DNA/RNA automated capillary electrophoresis, 48-capillary	VBCF
Automated (Hamilton STAR) library preparation (Lexogen autoQuantSeq)	VBCF

 

Diagnostics

Genomics Core Facility offers its services and access to instruments for genomic analysis mainly for scientific projects. Some capacity also provides for specialized diagnostic testing for the general public.