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Genomika és Bioinformatika

  • Szolgáltatások
  • Munkatársak
  • Publikációk

The Genomics and Bioinformatics Core Facility is the first Hungarian core facility with special emphasis of providing services on both next generation sequencing (NGS) and bioinformatics.

Located in the Szentágothai Research Centre at the University of Pécs, it offers a broad range of NGS services, including Illumina sequencing (NextSeq, MiSeq, MiniSeq and iSeq), nanopore long-read sequencing (MinION), and full-service protocols for genome, transcriptome, epigenome and metagenome sequencing. The facility also offers advice on study design and provide bioinformatics and biostatistical data analysis services on NGS data as well as other biomedical data.

Szolgáltatások

Library preparation and quality control

Tapestation 4200

The Genomics and Bioinformatics Facility offers a broad range of library preparation methods from DNA and RNA samples depending on the sequencing technology, sample source, and biological question of interest. At each step there is a careful quality check of each sequencing library prepared either by our facility staff members or the users. The major steps include:

  • Measurement of concentration (Fluorescence Qubit 4.0)
  • Measurement of size (Bioanalyzer 2100, TapeStation 4200)

Contact



Next generation sequencing

Sequencing is performed on Illumina (NextSeq 550, MiSeq, MiniSeq, iSeq) and Nanopore (MinION) sequencing instruments depending on the application and biological question. The available instruments cover short (Illumina technology) and long sequencing (Oxford Nanopore technology) as well as a broad range of output, from a few million to hundrends of millions reads.

Contact

NextSeq 550


Bioinformatics and data analyis

The facility provides bioinformatics services covering all the major steps of NGS data analysis, including data preprocessing (demultiplexing and transfer of unaligned BAM file), standard bioinformatic analysis (alignment and genome browser visualization of BAM file), downstream bioinformatic analysis (e.g. differential expression or genotype calling) as well as assistance with publication-related data sharing requirements (e.g. GEO submission).

Contact



Műszerek

Covaris M220 Ultrasonicator

Covaris M220

M220 Focused-ultrasonicator is designed for Next Generation Sequencing applications requiring fragment sizes between 150bp and 5kb. Covaris AFA transmits acoustic energy at ultrasonic frequencies and very short wavelengths and is uniquely able to focus the energy into your sample. AFA controls the shearing forces that fragment nucleic acids to the selected size.



Illumina iSeq NGS

The iSeq destkop sequencer utilizes Illumina’s one-channel sequencing by synthesis technology to give extraordinarily fast sequencing turnaround while maintaining high data quality. Even as the smallest Illumina sequencer to-date, it is still able to produce over 1.2 billion base pairs in as little as 9 hours for a 50-bp single-read run. The iSeq is a flexible system with a wide range of applications that is ideal small genome sequencing, targeted and amplicon sequencing, and viral and microbial sequencing.

iSeq


Illumina MiniSeq

MiniSeq

The MiniSeq System provides high-quality sequencing technology with the cost-effective desktop system. It enables small genome, amplicon, targeted enrichment, and RNA sequencing using low library volume. It is ideal for targeted research applications like cancer sequencing and gene expression profiling.



Illumina MiSeq

The MiSeq benchtop instrument utilizes a double-sided, single-lane flow cell and reagent cartridge supplied in kit form. It performs both single- and paired-end runs with adjustable read lengths from 1 x 36 base pairs to 2 x 300 base pairs. MiSeq is also a cost-effective tool for various analyses focused on targeted gene sequencing (amplicon sequencing or target enrichment), metagenomics, and gene expression studies.

MiSeq


Illumina NextSeq 550 NGS

NextSeq 550

The NextSeq 550 System offers the right sequencer for various project sizes and sequencing throughputs, providing users with optimal operational efficiency. This fast, flexible, high-throughput benchtop sequencer enables transcriptome and targeted resequencing applications with the accuracy of Illumina sequencing technology. With the ability to switch between lower and higher run configurations based on a project’s needs, the NextSeq 550 is the ideal platform for small to medium sequencing projects that range in output requirements.



Oxford Nanopore MinION sequencer

MinION is a portable, real-time device for DNA and RNA sequencing, putting you in control of your sequence data. Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the fragmentation, the need for PCR amplification or chemical labeling of the sample. Ultra-long read lengths are possible (hundreds of kb) as you can choose your fragment length.

Nanopore MinIon


TapeStation 4200 system

Tapestation 4200

The Agilent 4200 TapeStation system is intended to separate nucleic acids by means of electrophoresis. This instrument is a complete solution for true end-to-end sample QC within any NGS workflow covering the full DNA and RNA sizing range. Depending on your application, the software automatically determines size, quantity, purity, RNA and DNA integrity.



Hasznos tudnivalók

Usage policy and facility access

The Genomics and Bioinformatics facility offers access to its services to all Hungarian academic and industrial research groups. Free capacity is offered to other external users (academic and industry) of other countries. To estimate feasibility and allocable resources, we strongly recommend contacting our team when planning a sequencing experiment or bioinformatics data analysis task.

 

Acknowledging the facility

Continuation of funding for the Genomics and Bioinformatics facility by the University of Pécs as well as the Hungarian and European funding agencies depends on documented evidence of contribution to scientific output. We therefore require acknowledgement of use of the facility in published work. A simple statement is sufficient and can either be placed in the Materials and Methods section or at the end of your manuscript (acknowledgements) depending on the journal format, such as:

Next generation sequencing and/or bioinformatics data analysis services were performed by the Genomics and Bioinformatics Core Faciity of the Szentágothai Research Centre at the University of Pécs.” Your publication will be also listed on our website.

Contact

Dr. Gyenesei Attila
tudományos főmunkatárs
gyenesei.attila@pte.hu
Bauer Witold
tudományos segédmunkatárs
bauer.witold@pte.hu
Gálik Bence
tudományos segédmunkatárs
galik.bence@pte.hu
Dr. Herczeg Róbert
kutató
herczeg.robert@pte.hu
Dr. Kun József
tudományos munkatárs
jkun80@gmail.com
35404
Urbán Péter
PhD hallgató
urban.peter@pte.hu

2019

Publikációk

  • Marik T, Tyagi C, Balázs D, Urbán P, Szepesi Á, Bakacsy L, Endre G, Rakk D, Szekeres A, Andersson M A, Salonen H, Druzhinina I S, Vágvölgyi Cs, Kredics L. Structural Diversity and Bioactivities of Peptaibol Compounds From the Longibrachiatum Clade of the Filamentous Fungal Genus Trichoderma. Frontiers in Microbiology, 2019. Accepted for publication. Doi: 10.3389/fmicb.2019.01434. IF: 4.26
     
  • Garai K, Ádam Z, Herczeg R, Katai E, Nagy T, Pál Sz., Gyenesei A, Pongracz J, Wilhelm M, Kvell K. Artificial neural network correlation and biostatistics evaluation of physiological and molecular parameters in healthy young individuals performing regular exercise. Frontiers in Physiology, 2019. Accepted for publication. IF: 3.2
     
  • Péterfalvi A, Németh N, Herczeg R, Tényi T, Miseta A, Czéh B, Simon M. Examining the Influence of Early Life Stress on Serum Lipid Profiles and Cognitive Functioning in Depressed Patients. Frontiers in Psychology 2019. Accepted for publication. https://doi.org/10.3389/fpsyg.2019.01798, IF: 2.13
     
  • Gángó A*, Alpár D*, Gálik B*, Marosvári D, Kiss R, Fésüs V, Aczél D, Eyüpoglu E, Nagy N, Nagy Á, Krizsán S, Reiniger L, Farkas P, Kozma A, Ádám E, Tasnády S, Réti M, Matolcsy A, Gyenesei A, Mátrai Z, Bödör C. Dissection of Subclonal Evolution by Temporal Mutation Profiling in Chronic Lymphocytic Leukemia Patients Treated With Ibrutinib. International Journal of Cancer 2019 Jun 10. Doi: 10.1002/ijc.32502. IF: 7.36
     
  • Bauer W, Veijola R, Lempainen J, Kiviniemi M, Härkönen T, Toppari J, Knip M, Gyenesei A*, Ilonen J*. Age at Seroconversion, HLA Genotype and Specificity of Autoantibodies in Progression of Islet Autoimmunity in Childhood. Journal of Clinical Endocrinology & Metabolism 2019 May 23. pii: jc.2019-00421. doi: 10.1210/jc.2019-00421. IF: 5.79
     
  • Zana B, Geiger L, Kepner A, Földes F, Urbán P, Herczeg R, Kemenesi G, Jakab F. First molecular detection of Apis mellifera filamentous virus in honey bees ( Apis mellifera ) in Hungary, Acta Veterinaria 2019, 67:1 pp. 151-157. IF: 1.04
     
  • Montskó, G ; Gödöny, K ; Herczeg, R ; Várnagy, Á ; Bódis, J ; Kovács, GL Alpha-1 chain of human haptoglobin as viability marker of in vitro fertilized human embryos: information beyond morphology. System Biology in Reproductive Medicine 2019, 65: 2 pp. 174-180, IF: 1.58
     
  • Aczél T, Kun J, Szőke É, Rauch T, Junttila S, Gyenesei A, Bölcskei K, Helyes Zs. Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. Frontiers in Molecular Neuroscience 2018. Doi: 10.3389/fnmol.2018.00219. IF: 3.90
  • Bödör C, Alpár D, Marosvári D, Galik B, Rajnai H, Bátai B, Nagy Á, Kajtár B, Burján A, Deák B, Schneider T, Alizadeh H, Matolcsy A, Brandner S, Storhoff J, Chen N, Liu M, Ghali N, Csala I, Bagó AG, Gyenesei A, Reiniger L. Molecular Subtypes and Genomic Profile of Primary Central Nervous System Lymphoma. J Neuropathol Exp Neurol. 2019 Nov 28. doi: 10.1093/jnen/nlz125. 

2020

Publikációk

  • Gángó A, Alpár D, Galik B, Marosvári D, Kiss R, Fésüs V, Aczél D, Eyüpoglu E, Nagy N, Nagy Á, Krizsán S, Reiniger L, Farkas P, Kozma A, Ádám E, Tasnády S, Réti M, Matolcsy A, Gyenesei A, Mátrai Z, Bödör C. Dissection of subclonal evolution by temporal mutation profiling in chronic lymphocytic leukemia patients treated with ibrutinib. Int J Cancer. 2020 Jan 1;146(1):85-93. doi: 10.1002/ijc.32502.
     
  • Montgomery SA, Tanizawa Y, Galik B, Wang N, Ito T, Mochizuki T, Akimcheva S, Bowman JL, Cognat V, Maréchal-Drouard L, Ekker H, Hong SF, Kohchi T, Lin SS, Liu LD, Nakamura Y, Valeeva LR, Shakirov EV, Shippen DE, Wei WL, Yagura M, Yamaoka S, Yamato KT, Liu C, Berger F. :Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin. Current Biology 2020 Feb 24;30(4):573-588.e7. doi: 10.1016/j.cub.2019.12.015. 
     
  • Bödör C, Alpár D, Marosvári D, Galik B, Rajnai H, Bátai B, Nagy Á, Kajtár B, Burján A, Deák B, Schneider T, Alizadeh H, Matolcsy A, Brandner S, Storhoff J, Chen N, Liu M, Ghali N, Csala I, Bagó AG, Gyenesei A, Reiniger L. : Molecular Subtypes and Genomic Profile of Primary Central Nervous System Lymphoma. Journal of Neuropathology & Experimental Neurology 2020 Feb 1;79(2):176-183. doi:10.1093/jnen/nlz125.
     
  • Csepregi R, Temesfői V, Das S, Alberti Á, Tóth CA, Herczeg R, Papp N, Kőszegi T. :Cytotoxic, Antimicrobial, Antioxidant Properties and Effects on Cell Migration of Phenolic Compounds of Selected Transylvanian Medicinal Plants. Antioxidants (Basel). 2020 Feb 18;9(2):166. doi: 10.3390/antiox9020166. 
     
  • Paczkowska-Abdulsalam M, Niemira M, Bielska A, Szałkowska A, Raczkowska BA, Junttila S, Gyenesei A, Adamska-Patruno E, Maliszewska K, Citko A, Szczerbiński Ł, Krętowski A. : Evaluation of Transcriptomic Regulations behind Metabolic Syndrome in Obese and Lean Subjects. International Journal of Molecular Sciences 2020 Feb 20;21(4):1455. doi:10.3390/ijms21041455.
     
  • Fodor, István ; Zrinyi, Zita ; Urbán, Péter ; Herczeg, Robert ; Büki, Gergely ; M. Koene, Joris ; Tsai, Pei-San ; Pirger, Zsolt: Identification, presence, and possible multifunctional regulatory role of invertebrate gonadotropin-releasing hormone/corazonin molecule in the great pond snail (Lymnaea stagnalis)2020 doi: 10.1101/2020.03.01.971697
     
  • Madai M, Németh V, Oldal M, Horváth G, Herczeg R, Kelemen K, Kemenesi G, Jakab F. :Temporal Dynamics of Two Pathogenic Hantaviruses Among Rodents in Hungary. Vector-Borne and Zoonotic Diseases. 2020 Mar;20(3):212-221. doi: 10.1089/vbz.2019.2438.
     
  • Aczél T, Kecskés A, Kun J, Szenthe K, Bánáti F, Szathmary S, Herczeg R, Urbán P, Gyenesei A, Gaszner B, Helyes Z, Bölcskei K. : Hemokinin-1 Gene Expression Is Upregulated in Trigeminal Ganglia in an Inflammatory Orofacial Pain Model: Potential Role in Peripheral Sensitization. International Journal of Molecular Sciences 2020 Apr 22;21(8):2938. doi: 10.3390/ijms21082938. 
     
  • Papp H, Zeghbib S, Földes F, Banfai K, Madai M, Kemenesi G, Urbán P, Kvell K, Jakab F. :Crimean-Congo hemorrhagic fever virus infection triggers the upregulation of the Wnt signaling pathway inhibitor genes. Virus Genes 2020 Apr 25. doi: 10.1007/s11262-020-01759-z. 
     
  • Friston D, Junttila S, Lemes JBP, Laycock H, Torres-Perez JV, Want E, Gyenesei A, Nagy I.:  Leptin and fractalkine: novel subcutaneous cytokines in burn injury. Disease Models & Mechanisms 2020 Apr 29;13(4):dmm042713. doi: 10.1242/dmm.042713.
     
  • Kemenesi G, Kornya L, Tóth GE, Kurucz K, Zeghbib S, Somogyi BA, Zöldi V, Urbán P, Herczeg R, Jakab F. :Nursing homes and the elderly regarding the COVID-19 pandemic: situation report from Hungary. Geroscience. 2020 May 18:1-7. doi: 10.1007/s11357-020-00195-z. 
     
  • Fodor I, Urbán P, Kemenes G, Koene JM, Pirger Z. :Aging and disease-relevant gene products in the neuronal transcriptome of the great pond snail (Lymnaea stagnalis): a potential model of aging, age-related memory loss, and neurodegenerative diseases. Invertebrate Neuroscience 2020 May 24;20(3):9. doi: 10.1007/s10158-020-00242-6. 
     
  • Bodis J, Gödöny K, Várnagy Á, Kovács K, Koppán M, Nagy B, Erostyák J, Herczeg R, Szekeres-Barthó J, Gyenesei A, Kovács GL.:  How to reduce the potential harmful effects of light on blastocyst development during IVF. Medical Principles and Practice 2020 May 29. doi: 10.1159/000509016. 

2018

Publikációk

  • Mutti M, Sonnevend Á, Pál T, Junttila S, Ekker H, Galik B, Gyenesei A, Nagy G, Nagy E, Szijártó V. : Complete Genome Sequence of Escherichia coli 81009, a Representative of the Sequence Type 131 C1-M27 Clade with a Multidrug- Resistant Phenotype. Genome Announcements. 2018 doi: 10.1128/genomeA.00056-18. 

 

  • Aczél T, Kun J, Szőke É, Rauch T, Junttila S, Gyenesei A, Bölcskei K, Helyes Z. : Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. Frontiers in Molecular Neuroscience 2018 doi: 10.3389/fnmol.2018.00219. 

 

  • Datki Z, Olah Z, Hortobagyi T, Macsai L, Zsuga K, Fulop L, Bozso Z, Galik B, Acs E, Foldi A, Szarvas A, Kalman J. :Exceptional in vivo catabolism of neurodegeneration-related aggregates.  2018 Jan 29;6(1):6. doi: 10.1186/s40478-018-0507-3. 

 

  • Bán Á, Pintér E, Kun J. :A megfelelő szájegészség megvédhet a kalciumcsatorna- blokkoló készítmények okozta gingivahyperplasia kialakulásától [Proper oral health can protect from developing gingival hyperplasia induced by calcium channel blockers]. Orvosi Hetilap 2018 Jul;159(29):1183-1187. Hungarian. doi: 10.1556/650.2018.31088. 

 

  • Feller D, Kun J, Ruzsics I, Rapp J, Sarosi V, Kvell K, Helyes Z, Pongracz JE. : Cigarette Smoke-Induced Pulmonary Inflammation Becomes Systemic by Circulating Extracellular Vesicles Containing Wnt5a and Inflammatory Cytokines. Frontiers in Immunology. 2018 Jul 25;9:1724. doi: 10.3389/fimmu.2018.01724. 

 

  • Deutsch-Nagy L, Urbán P, Tóth Z, Bihari Z, Kocsis B, Fekete C, Kilár F. : Genome sequence of Shigella sonnei 4303. Gut Pathogens 2018 Oct 24;10:47. doi: 10.1186/s13099-018-0274-5. 
KAPCSOLAT
Dr. Gyenesei Attila
Core Facility Vezető
 
LETÖLTÉSEK
LINKEK
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Publikációk

  • Mutti M, Sonnevend Á, Pál T, Junttila S, Ekker H, Galik B, Gyenesei A, Nagy G, Nagy E, Szijártó V. : Complete Genome Sequence of Escherichia coli 81009, a Representative of the Sequence Type 131 C1-M27 Clade with a Multidrug- Resistant Phenotype. Genome Announcements. 2018 doi: 10.1128/genomeA.00056-18. 

 

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Publikációk

  • Gángó A, Alpár D, Galik B, Marosvári D, Kiss R, Fésüs V, Aczél D, Eyüpoglu E, Nagy N, Nagy Á, Krizsán S, Reiniger L, Farkas P, Kozma A, Ádám E, Tasnády S, Réti M, Matolcsy A, Gyenesei A, Mátrai Z, Bödör C. Dissection of subclonal evolution by temporal mutation profiling in chronic lymphocytic leukemia patients treated with ibrutinib. Int J Cancer. 2020 Jan 1;146(1):85-93. doi: 10.1002/ijc.32502.
     
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