GENOMICS

EATRIS-CZ brings small, medium, and medium-large sequencing and genotyping projects a step closer to reality. Despite the buzz about the low price of getting genetic information, starting a sequencing or genotyping project requires initial investment in millions of Euros, continuous education of staff not only in the wet part of laboratory work but also in bioinformatics, and uninterrupted stream of samples to keep instruments running. In many cases, outsourcing or collaborative research may be the most reasonable solution. 

Support of research/drug development projects

Within EATRIS-CZ infrastructure, we can offer services using a dozen of real time thermocyclers including 1536-wells format and droplet digital PCR (Bio-Rad QX200). Moreover, Affymetrix microarray device (Human Gene- and Exon- level expression, miRNA profiling, FFPE OncoScan, HD Cytoscan) and two next-generation sequencing platforms from Illumina (MiSeq, HiSeq) are installed there, with an access to NovaSeq platform.

The supported applications include

• SNP genotyping
• Amplicon sequencing for metagenomic studies
• Targeted sequencing of formalin fixed paraffin embedded (FFPE) samples
• Transcriptome sequencing
• Exon and/or whole genome sequencing
• Targeted detection of cytosine methylation by pyrosequencing and/or massively parallel sequencing
• miRNA and gene expression profiling

Other types of services/analyses offered

• Chromosomal microarrays (CMA)
• Constructing of DNA FISH probes for designated genes/chromosomal areas
• Fluorescent in situ hybridization (FISH)
• Genotyping, SNPs
• High Resolution Melting Analysis (HRM)
• Many types of PCR including ddPCR
• Circulating tumor cells detection and characterization
• Human papillomavirus (HPV) detection and full genotyping of high-risk and low-risk HPV genotypes
• Triage testing of HPV-positive women by methylation test

PROTEOMICS

EATRIS-CZ proteomics facilities feature a comprehensive set of analytical instruments to cover a broad range of proteomic analyses:
Orbitrap based mass spectrometers Elite and Fusion (Thermo Scientific) for discovery proteomics, QTrap 5500 (ABSciex) for protein quantitation and validation by single/multiple reaction monitoring (SRM/MRM). The facilities also offer an access to two MALDI-TOF UltrafleXtreme (Bruker Daltonics) systems.
Except of mass spectrometers, proteomics facilities offer Quadra3 liquid handling workstation (TOMTEC Life Sciences) for solid phase extraction, 1D, 2D, DIGE scanner Typhoon (GE), recombinant protein production and purification instrumentation NGC-Discover,
chromatography system (Bio-Rad) available to expedite a high-volume sample preparation and analysis.

The instrumentation is supported by data management and complex analyses systems that are administered by the cooperating bioinformatics & IT support staff.
Proteomics facilities of EATRIS-CZ partner institutes are able to perform a broad scale of experiments including protein identification and quantification in samples ranging from single
gel bands to whole cell lysates, serum or other biological fluids. Quality control of your samples and LC/MS method development can be done as well.

Support of research/drug development projects

• Protein identification, discovery, quantitation (labelled, label-free), SILAC, FAS
• Biomarker discovery, validation, SWATH, SRM, MRM, glycocapture
• Identification of protein post-translational modifications
• Immunoaffinity pull-down experiments, molecular targets identification
• Mass spectrometry data analyses
• Consultations, trainings

Advantages and options EATRIS-CZ proteomics facilities can bring to your research

• Access to a broad scale of high-end proteomic equipment including Orbitrap, MALDI-TOF,
• Q-TOF and other mass spectrometers connected with nano-LC
• Isotope labeling of proteins not affecting their function and behavior
• Seamless transition from cell-culture to tissue or serum experiments
• Precise targeted quantification with isotope labeled internal standards
• Robotic liquid handling reducing variability
• Both discovery and validation phase can be performed
• Advanced knowledge and methodic support

BIOBANKING

Biological samples and accompanying patient data are necessary for the development of any new drug or a diagnostic assay and consequently for advancing biomedical research in the context of personalized medicine.

EATRIS-CZ closely collaborates with another medical research infrastructure - European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI), providing strong support for translational research projects. Generally, the process of sample collection is marked with close collaboration between patients, surgeons, pathologists, researchers, and biobank personnel. Thus, obtaining a coherent cohort of clinically characterized samples may be behind reach of academic centers without direct contact to teaching hospitals.

Support of research/drug development projects

• EATRIS-CZ members provide direct access to samples from tumor collection that include:
• DNAs (more than 15,000 samples from 8,000 patients)
• RNAs (more than 4,000 samples from 3,000 patients)
• FFPE slices (more than 40,000 samples from 10,000 patients)
• Cryosamples (about 5,000 tissue samples from 1,000 patients with lung, brain, colorectal, breast, lymphatic node, ovary, testicle, prostate, and bone marrow diseases)
• Tissue samples fixed in RNA later (parallelly collected with tissue cryosamples)
• Other tissues samples through appropriate material transfer agreements

Collaborating facilities also provide infrastructure for the storage of frozen and deep-frozen samples, mostly from cancer patients. Among other technologies, the facilities offer capacity in liquid nitrogen cryosystems from Lineq equipped with Kesai alarm systems. Mowden -80 °C cryosystems are also available, and are equipped with CryoData2, Innova U725, and COMET software.