Instituto Superior Técnico, Universidade de Lisboa
Complex Data Facilities
Systems Biology/Computational Biology Facilities
Clinical Research Centres
Cell Culture Facilities
Collections of Biological Resources (e.g. Microorganisms, Biobanks and Seed Banks)
The Center for Clinical Genomics provides the research equipment used for genomic examinations and the special knowledge belonging to this, to the researchers of the University of Debrecen - Medical and Health Science Center and also to exterior procurers. The Center for Clinical Genomics provided the services listed below in the last period: Microarray service - this service was a "Sample in - Data out-type", fully comprehensive one, thus procurers only had to guarantee the Experiment Plan and the starting material and they received ready, analysable experimental data. Our main experience is global gene expression examinations. Platforms used: Applied Biosystems and Affymetrix microarray platforms. Our infrastructure is able to perform the whole work process from sample isolation through quality control to data analysis. TaqMan Low Density Array service - this service is used on different levels from accessing to research equipment to the whole analysis of data. It is mainly used for validation of microarray data. DNA sequencing and fragment analysis. The method is used for detecting unique DNA variants. The biobanking core facility has been used in several collaborative clinical genomics projects. We have recently established a next generation sequencing service.
The microarray facility is equipped with a high resolution versatile scanner which is suitable for capturing images in UV, VIS, luminescent and chemiluminescent mode, and with a special adapter for scanning microarray slides. The data obtained from the scans can be further assessed and processed by the high capacity computer workstation. The whole transcriptomics workflow and subsequent studies, such as the exploratory analysis by clustering, GO annotations, promoter extraction using in-house databases, the validation of microarray data by real-time PCR can be carried out in the laboratory. The research instruments, including light, stereo and electronmicroscopes, a micromanipulation workstation, cameras and image analysis softwares is suitable to perform structural and ultrastructural histological and cytological studies, and enables the detection of tissue-specific gene expression.
454 Sequencing can sequence any double-stranded DNA and enables a variety of applications including de novo whole genome sequencing, re-sequencing of whole genomes and target DNA regions, metagenomics and RNA analysis.
The Biorobot is able to print small molecules (oligonucleotides, proteins, drug-like compounds) onto a glass surface in high density. The high level of automation enables to fine tuning and standardization of numerous printing parameters like temperature inside the machine, humidity, space between the points, speed of the pins, washing conditions. The rapidity of the equipment is unique; it prints 120 points in 10 hours onto 100 glass plates. The sample capacity is 20 microtiter plates.
The Core Facility is able to measure one- and two-color genexpression microarray, miRNA array, and CGH (comparative genome hybridization) array. In Hungary this facility is one of the most thoroughly equipped microarray labs. Instruments: -Agilent 2100 Bioanalyzer - Agilent hybridization oven- Agilent Microarray Scanner + Feature Extraction Software, and GeneSpring GX11 Sofware.
Since the introduction of the Next-generation Sequencing (NGS) technology at the beginning of 2007, the technology became the leading source of the high-throughput, whole-genome analysis. NGS instruments can be utilized for the analysis of various bioligical samples, such as phylogenetic analysis of microbes, sequenciung after chromatin immunoprecipitation (ChIP-Seq), copy number variation. BAYGEN runs the latest, SOLiD V4 instrument of Applied Biosystems (part of Life Technologies) which utilizes a revolutionary technology: the DNA samples are ligated to a bead surface and the clonally amplified DNA fragments are analyzed using massively parallel sequencing. The sequencing reaction is based on ligation of fluorescently labeled oligonucleotides. The ultra-high throughput and accuracy as well as numerous application are making NGS system the leading force of genomics revolution.
The Applied Biosystems 7900HT Fast Real-Time PCR System is a high-throughput real-time PCR system that detects and quantitates nucleic acid sequences. The interchangeable fast 96, standard 96, and 384-well block capability combined with the Automation Accessory offers unmatched flexibility. Sample tracking is greatly simplified with the use of hand-held and integrated bar code readers. These features make the 7900HT system ideally suited to meet the high throughput requirements of today's drug discovery process. Key applications include gene expression quantitation and the detection of single nucleotide polymorphisms (SNPs) using the fluorogenic 5' nuclease assay. The 7900HT uses a Peltier-based thermal cycling system and an extended-life 488 nm argon-ion laser excitation source.
Computational pipeline for the identification and correction of the sequences of mispredicted genes. Database of mispredicted and corrected gene sequences. Functional genomics laboratory for experimental validation of corrected sequences.
After mapping the Human Genome the next milestone in the genomic researches is to reveal the function of the genetic elements. The promoter regions play a central role in the regulation of gene transcription. Our PromoterDB collects and visualizes the structural elements (intron exon, UTR region, EST, TSS) of human genes according to their genetic information, and it also highlights the sequence motifs of the known promoter regions. The database is continuously updated. Our next goal is to expand it to contain other organisms' genomes (primarily model organisms), and to develop novel motif searching algorithms that help the effective recognition of characteristic promoter patterns (TATA box, GC box, CAAT box, MTE, BRE, DPE, iniciator elements and octamers).