A Szentágothai János Kutatóközpont a PTE korszerű, nemzetközi tudományszervezési és menedzsment normák szerint kialakított új intézménye, amely az élettudományi, élettelen természettudományi, valamint környezettudományi oktatás...
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 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.
NovaSeq 6000 Sequencing System is designed to do it all. The system allows to sequence up to 48 genomes in ~2 days for the most comprehensive coverage. The workflow could be scalable up and down effortlessly with the improved economics so it is cost effective even for the small project. The NovaSeq 6000 sequencer is ideal for transciptomic, metagenomic, targeted and whole genome sequencing.
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.
The ABI PRISM® 310 sequencer is an automated single-capillary genetic analyzer designed for a wide range of sequencing and fragment analysis applications. Perform comparative sequencing, linkage analysis, STR analysis, SNP detection, discovery and validation, mutation detection, and many other applications. The sequencer detect five dyes simultaneously to increase throughput. The average test time for a sample is one and a half hours.
The StepOnePlus™ Real-Time PCR System is a 96-well Real-Time PCR instrument perfect for both first-time and experienced users. The StepOnePlus™ Real-Time PCR System can be setup in a variety of configurations and comes ready to use, out of the box, with intuitive data analysis and instrument control software. Utilizing robust LED based 4-color optical recording, the StepOnePlus™ Real-Time PCR System is designed to deliver precise, quantitative Real-Time PCR results for a variety of genomic research applications. The StepOnePlus™ Real-Time PCR System has an innovative Applied Biosystems VeriFlex Block for convenient PCR optimization.
CFX Real-Time PCR Detection Systems are powerful and flexible instruments, featuring 2–5 color multiplexing, advanced optical technology, and precise temperature control with thermal gradients. These systems deliver sensitive, reliable detection of both singleplex and multiplex real-time PCR reactions. Paired with CFX Maestro Analysis Software, CFX Instruments provide superior data collection, statistical analysis, and data visualization capabilities.
With the high capacity floor standing Hitachi centrifuge, maximum 6 L (4x1500 ml) can be centrifuged. The centrifuge can be operated easily with the help of an LCD touchscreen, and all the important parameter can be controlled and followed during centrifugation. Maximum speed is 22.000 rpm.
http://www.ibiotech.cz/media/files/product_pdf/cn22n.pdf
The nCounter SPRINT Profiler employs a novel digital barcode technology that hybridizes to target molecules. Each unique digital barcode is then directly counted using a single molecule imaging technique to yield precise and sensitive quantification. Up to 800 targets can be measured simultaneously in a single sample, and up to 12 samples can be assayed in a single run.
https://www.nanostring.com/products/ncounter-systems-overview/ncounter-sprint-profiler
The following nCounter applications are supported on the SPRINT Profiler:
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