A Szentágothai János Kutatóközpont a PTE korszerű, nemzetközi tudományszervezési és menedzsment normák szerint kialakított új intézménye, amely az élettudományi, élettelen természettudományi, valamint környezettudományi oktatás...
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.
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:
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.
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).
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.
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.
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.
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.
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.
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.
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.
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.
