Infrastructure

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Next generation sequencing

Illumina HiScanSQ

HiScanSQ integrates proven array and sequencing technologies. Sequencing by synthesis (SBS) is the basis of the HiScanSQ NGS platform. TruSeq technology supports massively parallel sequencing using a proprietary reversible terminator-based method that enables detection of single bases as they are incorporated into growing DNA strands. A fluorescently-labeled terminator is imaged as each dNTP is added and then cleaved to allow incorporation of the next base. Since all four reversible terminator-bound dNTPs are present during each sequencing cycle, natural competition minimizes incorporation bias. SBS technology supports both single read and paired-end libraries. It is the only platform that offers a short-insert paired-end capability for high-resolution genome sequencing as well as long-insert paired-end reads using the same robust chemistry for efficient sequence assembly, de novo sequencing and most importantly large-scale structural variation detection.

Illumina’s BeadArray Technology is based on 3-micron silica beads that self assemble in microwells on either of two substrates: fiber optic bundles or planar silica slides. Our efforts will be extended in the near future into the development of Bead Array applications that are also offered by the highly versatile HiScanSQ system.

Affymetrix

ABI Prism 3100Avant Capillary sequencer:

The ABI 3100Avant is a four-capillary sequencer instrument. It enables to sequence plasmids and purified PCR products up to 700bp. BigDye Terminator v3.1 cycle sequencing kit (Life Technologies) is used for the sequencing reactions and the capillary electrophoresis is performed in a 50 cm length of capillary.

Affymetrix microarray platform:

Affymetrix GeneChip System provides systems biology perspective for both expression profiling and DNA analysis. GeneChip 3000 7G System contains: GCS 3000 7G Scanner with Autoloader, FS450 Fluidic Station, and HO 645 Hibridization Oven.
Our system is capable of performing the following analysis:
  1. Global gene expression analysis of more than 20 species including human, mouse and rat and many other model organisms for biomedical research: 3’ IVT expression arrays and Whole-Transcript expression arrays (exon and gene arrays).
  2. Genotyping of Single Nucleotide Polymorphisms (SNP’s): SNP 6.0 arrrays
  3. Detection of chromosomal abnormalities: CytoScan HD arrays

Epigenetics

Diagenode IP Star

SX-8G IP-Star® Automated System performs fully-automated liquid handling, magnetic separation, and incubation, significantly accelerating the optimization process, while also enhancing assay quality and robustness -- all within the rapid timeframe researchers require. The SX-8G IP-Star processes sheared chromatin or DNA to deliver purified DNA ready for qPCR, amplification, microarray and sequencing (e.g. Illumina™) analysis.

Tecan Freedom Evo

The Freedom EVO series offers precision, reliable liquid handling and easy-to-use robotics. Each platform can be combined with a wide choice of robotic arms, liquid handling tools and application options powered by straightforward software to meet your individual needs. The upgradeable Freedom EVO platform can evolve with your changing application needs making your initial investment even more valuable. Select the best pre-configured automation solution for your laboratory or create your own individual system according to your specific needs together with our automation specialists.
Tecan’s multi channel arm module has a 96-channel pipetting head that brings higher productivity to almost any automated liquid handling process, from drug discovery and compound management to biotechnology or genomics applications. The multi channel arm works in parallel with other arms of Freedom EVO®. For example processing a set of plates while the robotic manipulator arm brings the next set onto the worktable.
The multi channel arm can also operate as an 8- or 12-channel head as desired, picking a column of 8 or a row of 12 tips to perform for example, in-plate serial dilution for IC50 assays. It works with various disposable and washable tips and can exchange them automatically during a run.
It has a gripper on the pipetting head to allow moving plates, tip racks and assemble Tecan SPE module Te-VacS™.

Biobanking

The Genomics Center has expertise in the following areas pertaining to biobanking:

1. Organizing clinical sample collections and processing, in close collaboration with the clinics

Uniform and reliable sample collections are based on well-founded enrollment criteria and standard operating procedures (SOP) for collecting, transporting and processing of samples. Initial phase of the biobanking effort is devoted to establishing the enrollment criteria and SOPs. If needed, the Genomics Center provides training for nurses for more specialized sample collection procedures.

2. Sample processing and storage

The Genomics Center has the infrastructure and expertise to process clinical samples by a variety of techniques, from simple aliquoting of biofluids before storage to more advanced protocols, including: antibody-based cell sorting by MACS, Ficoll or Percoll-based centrifugal separation of cell subpopulations, preparation of cytospin slides, isolation of RNA and DNA, or archiving of solid tissue samples. Depending on the processing protocol and sample numbers, samples can be processed one by one, or in batches by high-throughput methods, using robotics. Samples can be stored at various temperatures; labile samples are stored either at -70?C in ultralow freezers, or in liquid N2 storage tanks at the Genomics Center. Samples are barcoded before storage, and information about the different collections is warehoused in the FreezerWorks software.

3. Research infrastructure

The Genomics Center has 26 m2 laboratory space dedicated for biobanking, a cold room, and a room for ultralow freezers and lN2 storage tank. In addition to standard molecular biology equipment we have the following specialized instruments: five ultralow freezers with CO2 backup and cell-phone-connected alarm system, a lN2 storage tank (storage capacity: 8000 vials), two QiaCube nucleic acid isolation robots, and Tecan pipetting robots for high-throughput sample processing and 96/384-well plate assembly.

Protein and cell engeneering

Tissue culture facility

In the cell culture lab we are routinely growing HEK and CHO cells at laboratory scale in T175 flasks,Corning Hyperflasks, Integra CELLine bioreactors, Integra Cell Roll bottles, and potentially a Sartorius A Plus 2L cell fermenter. We have, among other equipment, a NuAire Class II and a BioAir BIO II A biological safety cabinet, NuAire and Memmert CO2 incubators, HERMLE cell centrifuge. We use and have access to a FACS Calibur (Becton Dickinson), a FACS Aria (Becton Dickinson) Multilaser Cell Sorter, and a FACS Array (Becton Dickinson), equipments, as well as an Olympus Fluoview FV1000 confocal microscope for cell analysis within the campus.

Protein purification and characterisation facility

The laboratory is equipped with the Bio-Rad PROFINIA automated protein affinity purification system, and routinely use the following cartridges:Bio-Scale Mini Profinity IMAC Ni-affinity (1 ml, 5 ml), Bio-Scale Mini Profinity GST affinity (1 ml, 5 ml), UnoSphere SUPrA protein-A affinity (1 ml, 5 ml), UNOsphere Q anion-exchange (1 ml, 5 ml), UNOsphere Q cation-exchange (1 ml, 5 ml), CHT type I cation-exchange (1, 5ml) Bio-Gel P-6 desalting (10, 50 ml), We also have a GE Healthcare AKTA Basic FPLC/HPLC chromatografic system with fraction collection, on which we can do waxing of affinity purified protein samples, e.g. using a Bio-Rad Bio-Scale CHT2-I Column, 7 x 52 mm, or a GE Healthcare Mono-Q column, 1 ml. We have a high-peed benchtop Thermo Scientific/Heraeus Multifuge X3R refrigated centrifuge with fxed angle and swingout rotors with capacities for 250ml, 50 ml, and 15 ml tubes.
For protein biochemical and characterisation, we use protein electrophoresis (SDS-PAGE), Western blotting, ELISA-based quantification, Invitrogen Q-BIT fluorescence-based protein concentration measeurements. We have a large capacity for these analyses, with a good number of Bio-Rad Mini Protean Tetracell, Mini Protean III, and Mini Protean II protein electrophoresis cells, also, with a Protean II normal size apparatus, using Bio-Rad PowerPack HC and Basic power supplies, and a number of Bio-Rad Mini Trans-Blot Cell, a Bio-Rad Gel Dryer as well as a Bio-Rad MultiScreen apparatus for Western blotting and screening, and currently a Dynamica LEDETECT ELISA reader. We are also set up for, optimised and operating several various biological assays for recombinant cytokines (e.g. TF-1 assay for hGM-CSF, hIL-4, or M1 assay for hLIF) and therapeutic antibodies (e.g. ADCC).

Bacterial culture facility

The bacterial culture lab is equipped with a SANYO floor-standing shaker, a SANYO and a Memmert bacterial incubator, We have all the general molecular biology equipment for cloning and expression work, including ABI Thermal Cycler, BTX Electroporator, and Bio-Rad Mini Subcell DNA electrophoresis cell. We have access to refrigated floor-standing incubator capacity, as well as up to 100 L scale fermentation facility within the university for expression optimisation and scale-up.