ProGenTomics offers a wide range of proteomics and genomics services and support to the academic community and its external customers. We aim to tailor our services to the needs of our collaborators and customers, while giving great support.

What can we do for you?

Proteomics

We offer different services to separate, identify and quantify proteins in your sample, both in a gel-based and gel-free manner.

Genomics

From analysis of one or a few genes by qPCR or RT-qPCR, to high-throughput analysis of the whole genome, transcriptome or epigenome with next-generation sequencing.

Cell-based techniques

Our cell-based techniques services include everything to culture your cells, characterize them by laser microdissection microscopy or flow cytometry, or even purify them.

Bioinformatics

Bioinformatics analysis of high-dimensional data remains a challenge for most researchers. We can help you with this. We also developped some scripts and tools for your own use.

A little taste of some past projects

An overview of some of our projects. Click on a project to get more information.

Proteomics

Identification of the protein corona of (co)polymercoated gold nanoparticles
The design of engineered gold nanoparticles that can interact with living cells and tissues is important for many biomedical applications, including imaging, diagnostics, and drug delivery. Polymer-decoration of goldNP is attractive to modulate the goldNP properties and to render them colloidally stable in complex media. Also proteins can show different binding properties according to the polymer that is attached to the goldNP. To further investigate this, HEA x MEA y @goldNP were exposed to Foetal bovine serum. Subsequently, the particels were loaded on polyacrylamide gel (PAGE) and subjected to electrophoresis followed by in-gel digestion with trypsin. The bound proteins were identified by means of LC-MS/MS. Additionally, the hydrophobicity of the absorbed proteins was analysed by means of the GRAVY score.

Tailoring Cellular Uptake of Gold Nanoparticles Via the Hydrophilic-to-Hydrophobic Ratio of their (Co)polymer Coating
By: Zhang, Zhiyue; Van Steendam, Katleen; Maji, Samarendra; et al.
ADVANCED FUNCTIONAL MATERIALS, 25(22): 3433-3439, JUN 2015, DOI: 10.1002/adfm.201500904
Determination of autoimmune response after vaccination of Bearded Dragons against Devriesea agamarum
Cell lysate from Devriesea agamarum was separated on two dimensional (2D) gel-electrophoresis and stained with Sypro Ruby. In parallel a 2D Western blot was prepared. Immunodetection with serum antibodies and their corresponding secundary and tertiary antibody revealed several immunoreactive spots on Western blot. These spots were excised from the gel and identified by means of mass spectrometry. Aminoacid sequences were matched by Mascot Daemon using the in-house sequenced genome from Devriesea agamarum.

Autovaccination confers protection against Devriesea agamarum associated septicemia but not dermatitis in bearded dragons (Pogona vitticeps)
By: Hellebuyck, T; Van Steendam, K; Deforce, D; Blooi, M; Van Nieuwerburgh, F; Bullaert, E; Ducatelle, R; Haesebrouck, F; Pasmans, F; Martel, A.
PLoS One, 9(12): e113084, DEC 2014, DOI: 10.1371/journal.pone.0113084
Mass spectrometry-based proteomics as a tool to identify biological matrices in forensic science
In forensic casework analysis, identification of the biological matrix and the species of a forensic trace, preferably without loss of DNA, is of major importance. The biological matrices that can be encountered in a forensic context are blood (human or non-human), saliva, semen, vaginal fluid, and to a lesser extent nasal secretions, feces, and urine. All these matrices were applied on swabs and digested with trypsin in order to obtain peptides. These peptides were injected on a mass spectrometer (ESI Q-TOF) resulting in the detection of several biomarkers that were used to build a decision tree for matrix identification. Additionally, by means of this proteomic approach, species identification was possible. This approach has the advantage that the analysis is performed on the first "washing" step of the chelex DNA extraction, a solution which is normally discarded, and that one single test is sufficient to determine the identity and the species of the biological matrix, while the conventional methods require cascade testing.

Mass spectrometry-based proteomics as a tool to identify biological matrices in forensic science
By: Van Steendam K, De Ceuleneer M, Dhaenens M, Van Hoofstat D, Deforce D.
INTERNATIONAL JOURNAL OF LEGAL MEDICINE, 127(2): 287-298, MAR 2013, DOI: 10.1007/s00414-012-0747-x
Prenylated chalcone xanthohumol associates with histones in breast cancer cells - a novel target identified by a monoclonal antibody
The design of engineered gold nanoparticles that can interact with living cells and tissues is important for many biomedical applications, including imaging, diagnostics, and drug delivery. Polymer-decoration of goldNP is attractive to modulate the goldNP properties and to render them colloidally stable in complex media. Also proteins can show different binding properties according to the polymer that is attached to the goldNP. To further investigate this, HEA x MEA y @goldNP were exposed to Foetal bovine serum. Subsequently, the particels were loaded on polyacrylamide gel (PAGE) and subjected to electrophoresis followed by in-gel digestion with trypsin. The bound proteins were identified by means of LC-MS/MS. Additionally, the hydrophobicity of the absorbed proteins was analysed by means of the GRAVY score.

Prenylated chalcone xanthohumol associates with histones in breast cancer cells--a novel target identified by a monoclonal antibody
By: Wyns C, van Steendam K, Vanhoecke B, Deforce D, Bracke M, Heyerick A.
MOLECULAR NUTRITION & FOOD RESEARCH, 56(11): 1688-1696, NOV 2012, DOI: 10.1002/mnfr.201200030
Citrullinated vimentin as an important antigen in immune complexes from synovial fluid of rheumatoid arthritis patients with antibodies against citrullinated proteins
In order to identify the antigens in immune complexes in synovial fluid from patients with rheumatoid arthritis, the immune complexes were first isolated by means of protA and G columns. The eluted fraction was separated by means of two dimensional gel-electrophoresis and immunodetection on nitrocellulose membranes revealed the presence of vimentin and fibrinogen. In addition, by means of Western blotting, citrullination of vimentin was found as a characteristic post-translational modification.

Citrullinated vimentin as an important antigen in immune complexes from synovial fluid of rheumatoid arthritis patients with antibodies against citrullinated proteins
By: Van Steendam K, Tilleman K, De Ceuleneer M, De Keyser F, Elewaut D, Deforce D.
ARTHRITIS RESEARCH & THERAPY, 12(4): R132, 2010, DOI: 10.1186/ar3070

Genomics

In vivo study of Dicer-2-mediated immune response of the small interfering RNA pathway upon systemic infections of virulent and avirulent viruses in Bombus terrestris
Recent studies suggest a potent role of the small interfering RNA (siRNA) pathway in the control of bee viruses and its usefulness to tackle these viral diseases. However, the involvement of the siRNA pathway in the defense against different bee viruses is still poorly understood. Therefore, in this study, we comprehensively analyzed the response of the siRNA pathway in bumblebees of Bombus terrestris to systemic infections of the virulent Israeli acute paralysis virus (IAPV) and the avirulent slow bee paralysis virus (SBPV). Our analysis included quantification of abundance of the siRNA core gene expression levels, deep sequencing to examine virus-derived small RNAs, and use of an “RNAi-of-RNAi” approach to determine the effects of a reduced expression of Dicer-2, a core component of the RNAi machinery on viral titers.

In vivo study of Dicer-2-mediated immune response of the small interfering RNA pathway upon systemic infections of virulent and avirulent viruses in Bombus terrestris
By: Niu J, Smagghe G, De Coninck D, Van Nieuwerburgh F, Deforce D, Meeus I.
INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY, 70: 127-137, MAR 2016, DOI: 10.1016/j.ibmb.2015.12.006

Suboptimal culture conditions induce more deviations in gene expression in male than female bovine blastocysts

Since the development of in vitro embryo production in cattle, different supplements have been added to culture media to support embryo development, with serum being the most popular. However, the addition of serum during embryo culture can induce high birthweights and low viability in calves (Large Offspring Syndrome). Analysis of global gene expression in bovine embryos produced under different conditions can provide valuable information to optimize culture media for in vitro embryo production. We used RNA sequencing to examine the effect of in vitro embryo production, in either serum-containing or serum-free media, on the global gene expression pattern of individual bovine blastocysts.

Suboptimal culture conditions induce more deviations in gene expression in male than female bovine blastocysts
By: Heras S, De Coninck D, Van Poucke M, Goossens K, Bogado Pascottini O, Van Nieuwerburgh F, Deforce D, De Sutter P, Leroy JL, Gutierrez-Adan A, Peelman L, Van Soom A.
BMC GENOMICS, 17(1): 72, JAN 2016, DOI: 10.1186/s12864-016-2393-z

Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts

Chromosomal abnormalities in early embryonic development can give rise to implantation failure, early spontaneous abortions and/or fetuses with multiple congenital anomalies. For couples with a known balanced or unbalanced chromosomal rearrangement, preimplantation genetic diagnosis (PGD) can be offered against unbalanced chromosomal aberrations in the embryo during assisted reproductive technology (ART). At the same time, it is well established that early-stage embryos suffer from a high rate of (mosaic) aneuploidy, reducing embryo survival, implantation potential, and hence the success rate of ART. While many techniques (FISH, aCGH) are used to screen for chromosomal imbalances in embryos, we investigated the potential of shallow whole genome sequencing for this screening. To this end a few cells were isolated from the blastocyst, their DNA was amplified and sequenced at a low (about 0.1x) coverage.

Shallow whole genome sequencing is well suited for the detection of chromosomal aberrations in human blastocysts
By: Deleye L, Dheendene A, De Coninck D, Sante T, Christodoulos C, Heindryckx B, Van den Abbeel E, De Sutter P, Deforce D, Menten B, Van Nieuwerburgh F
FERTILITY AND STERILITY, 104(5): 1276-1285, NOV 2015, DOI: 10.1016/j.fertnstert.2015.07.1144

16S rRNA Amplicon sequencing demonstrates that indoor-reared bumblebees (Bombus terrestris) harbor a core subset of bacteria normally associated with the wild host
A MiSeq multiplexed 16S rRNA amplicon sequencing of the gut microbiota of wild and indoor-reared Bombus terrestris (bumblebees) confirmed the presence of a core set of bacteria, which consisted of Neisseriaceae (Snodgrassella), Orbaceae (Gilliamella), Lactobacillaceae(Lactobacillus), and Bifidobacteriaceae (Bifidobacterium). In wild B. terrestris we detected several non-core bacteria having a more variable prevalence. Although Enterobacteriaceae are unreported by non next-generation sequencing studies, it can become a dominant gut resident. Furthermore the presence of some non-core lactobacilli were associated with the relative abundance of bifidobacteria. This association was not observed in indoor-reared bumblebees lacking the non-core bacteria, but having a more standardized microbiota compared to their wild counterparts.

16S rRNA Amplicon sequencing demonstrates that indoor-reared bumblebees (Bombus terrestris) harbor a core subset of bacteria normally associated with the wild host
By: Meeus I, Parmentier L, Billiet A, Maebe K, Van Nieuwerburgh F, Deforce D, Wäckers F, Vandamme P, Smagghe G.
PLOS ONE, 10(4): e0125152, APR 2015, DOI: 10.1371/journal.pone.0125152
Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1)
Whole exome sequencing is a technique that aims to selectively sequence all exons of protein-coding genes. A canine whole exome sequencing enrichment kit was designed based on the latest canine reference genome (build 3.1.72). Its performance was tested by sequencing 2 exome captures, each consisting of 4 pre-capture pooled, barcoded Illumina libraries on an Illumina HiSeq 2500. At an average sequencing depth of 102x, 83 to 86% of the target regions were completely sequenced with a minimum coverage of five and 90% of the reads mapped on the target regions. Additionally, it is shown that the reproducibility within and between captures is high and that pooling four samples per capture is a valid option. Overall, we have demonstrated the strong performance of this WES enrichment kit and are confident it will be a valuable tool in future disease association studies.

Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1)
By: Broeckx B, Coopman F, Verhoeven G, Bavegems V, De Keulenaer S, De Meester E, Van Nieuwerburgh F, Deforce D.
SCIENTIFIC REPORTS, 4: 5597, JUL 2014, DOI: 10.1038/srep05597
Adequate reference genes for human embryonic stem cell RT-qPCR analysis
technical variation induced along the experimental procedure. One way to do this, is the use of multiple reference genes, which are stably expressed throughout all samples analyzed. However, the selection of these references is not always straightforward. For example, when studying human embryonic stem cell (hESC) differentiation, the differentiation process itself might influence reference gene expression stability and render commonly used reference genes not to be the most adequate references anymore. In our experimental setup, we compared 12 candidate-references for retinoic acid-induced differentiating hESC with the geNorm algorithm. It was indeed proven that GAPDH, ACTB and PPIA were not amongst the most stable reference loci; instead, B2M, RPL13A and Alu repeats proved to be the most suitable genes. This again indicates that a reference stability analysis is required for each new experimental setting.

Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells
By: Vossaert L, O’Leary T, Van Neste C, Heindryckx B, Vandesompele J, De Sutter P, Deforce D.
BMC MOLECULAR BIOLOGY, 14:21, SEP 2013, DOI: 10.1186/1471-2199-14-21

About ProGenTomics

ProGenTomics, located in Gent (Belgium), offers a wide range of proteomics and genomics services and support to the academic community and its external customers. We aim to tailor our services to the needs of our collaborators and customers, while giving great support.  

Contact us

ProGenTomics, proteomics & genomics services

  Ghent University, Faculty of Pharmaceutical Sciences

  Ottergemsesteenweg 460, 9000 Gent, Belgium

 

  +32 9 264 83 56