University of Szeged
Dept. Biochemistry and Molecular Biology

Genomics/sequencing lab


The genomics lab houses an Illumina MiSeq NGS sequencer suitable for various genomic and functional genomic applications. Various auxiliary equipment are also available.

MiSeq bench-top sequencers allow the longest sequencing read lengths (2x300 nucleotides) among the market leading Illumina sequencers. MiSeq supports paired-end sequencing; the maximum output per sequencing run is 15 Gb. Sequencing parameters, such as sequencing depth and read length can be set in wide ranges (1M - 25M sequencing reads per run and 2x50 - 2x300 nucleotides per read, respectively) by selecting suitable flow cells and reagent cartridges.

MiSeq is suitable for several genomic and functional genomic applications, such as:

  • de novo bacterial genome sequencing
  • targeted re-sequencing
  • metagenomics (16S amplicon sequencing)
  • SNP analysis
  • RNA-sequencing / transcriptomics
  • miRNA analysis
  • ChIP-seq

Other auxiliary equipment in the lab:

  • Covaris M220 ultrasonicator
  • Agilent Bioanalyzer 2100 capillary electrophoresis equipment
  • Thermo Scientific PikoReal 96 and ABI 7500 real-time PCR systems
  • Qubit 2.0 fluorometer
  • NanoDrop spectrophotometer
  • SciGene Hybex Microsample Incubator
  • Biosan MPS-1 Multiplate shaker
  • Biosan UVT-B-AR PCR cabinet


In case you are interested in the services of the lab either in the form of research cooperation or as a service, please write to Dr Laszlo Bodai.



References:

Genetic, epigenetic and transcriptional comparison of esophagus tumor-associated and adjacent normal myofibroblasts.
Huliák I, Bodai L, Czepán M, Kovács D, Szabó A, Tiszlavicz L, Lázár G, Rakonczay Z Jr, Hegyi P, Boros IM, Kiricsi M.
Oncol Rep. 2019. 41(2):839-852. doi: 10.3892/or.2018.6909.

Echinocandin-Induced Microevolution of Candida parapsilosis Influences Virulence and Abiotic Stress Tolerance.
Papp C, Kocsis K, Tóth R, Bodai L, Willis JR, Ksiezopolska E, Lozoya-Pérez NE, Vágvölgyi C, Mora Montes H, Gabaldón T, Nosanchuk JD, Gácser A.
mSphere. 2018. 3(6). pii: e00547-18. doi: 10.1128/mSphere.00547-18.

Drosophila small ovary gene is required for transposon silencing and heterochromatin organisation and ensures germline stem cell maintenance and differentiation.
Jankovics F, Bence M, Sinka R, Faragó A, Bodai L, Pettkó-Szandtner A, Ibrahim K, Takács Z, Szarka-Kovács AB, Erdélyi M.
Development. 2018. pii: dev.170639. doi: 10.1242/dev.170639.

Analysis of Drosophila melanogaster testis transcriptome.
Vedelek V, Bodai L, Grézal G, Kovács B, Boros IM, Laurinyecz B, Sinka R.
BMC Genomics. 2018. 19(1):697. doi: 10.1186/s12864-018-5085-z.

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis.
Chakraborty T, Thuer E, Heijink M, Tóth R, Bodai L, Vágvölgyi C, Giera M, Gabaldón T, Gácser A.
Virulence. 2018. 9(1):1019-1035. doi: 10.1080/21505594.2018.1475797.




Department of Biochemistry and Molecular Biology, University of Szeged
2013-2019.