Wednesday, 16 Oct 2019
 
 

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SERVICE OF OMICS AND SYSTEMS BIOLOGY FOR TRANSLATIONAL RESEARCH PDF Print E-mail
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THE GENOMIC ILLUMINA FACILITY

 

 

Core facility description:

The Illumina platform 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. When randomly assembled on one of these two substrates, the beads have a uniform spacing of ~5.7 microns. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide that act as the capture sequences in one of Illumina’s assays. The Illumina platform is the elective tool for studying the genome and transcriptome through DNA microarrays and next-generation sequencing.

BeadArray technology is deployed on either of two multi-sample array formats for DNA or RNA-analysis applications.

Special DNA microarrays are the SNP microarray, that are used to identify the so-called hypervariable traits, or those sequences that vary from individual to individual within the same species or subpopulations isolated geographically or socially. The arrays are then used to identify single nucleotide polymorphisms (SNPs), which are thought responsible for genetic variations and individual susceptibility to certain diseases. The DNA microarray can also be used for genotyping used in forensic medicine (DNA testing), the diagnostics and pharmacogenomics, a new branch of pharmacology, which aims to study the relationship between genetic diversity and response to drugs, intending to answer both the therapeutic effect or adverse side effects. The SNP microarrays are also used to track the profiles of somatic mutation in cancer cells. The amplifications and deletions, to which these cells are subject, can be investigated simultaneously with the comparative genomic hybridization technology.

The Illumina platform also includes a sequencing module "next generation".  Illumina’s sequencing by synthesis (SBS) technology is the most successful and widely-adopted next-generation sequencing platform worldwide. 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. In the Illumina Sequencing technology, 80 million or more single-molecule templates are immobilized on a proprietary flow cell surface designed to present the DNA in a manner that facilitates access to enzymes, while ensuring high stability of surface-bound template and low non-specific binding of fluorescently labeled nucleotides. Solid-phase amplification is employed to create up to 1,000 identical copies of each single molecule in close proximity (diameter of one micron or less). Therefore, this new technology offers a highly efficient, accurate and scalable solution that sets a new standard for productivity, cost and accuracy among next-generation sequencing technologies.

 

Expertise and services for Institutions and Industries:

  • Global analysis of gene expression for human RNA, or other species, based on information derived from the National Center for Biotechnology Information Reference Sequence (RefSeq NCBI) database, including genes, gene candidates, and splice variants;
  • Genome-wide expression profiles from low-abundance or partially-degraded human RNA samples, especially those from formalin-fixed, paraffin-embedded (FFPE) tissues. It provides a high-multiplex, low-cost array solution from the simultaneous profiling of over 29,000 transcripts. The assay combines the unique PCR and labeling steps from Illumina's DASL Assay with gene-based hybridization and the whole-genome probe set. Highly reproducible expression profiles (r2  >0.97) can be produced from as little as 10–100 ng total RNA from fresh frozen tissue or 50–200 ng total RNA from FFPE samples.
  • Whole-genome scanning for efficient, high-throughput analysis of genetic and structural variations, SNP genotyping and Copy Number Variation
  • Genome-wide methylation profiles using Infinium Methylation Assays quality that can interrogate 27,578 CpG loci corresponding to more than 14,000 genes with a single-nucleotide level resolution to deliver high-throughput power while minimizing the cost per sample.
  • DNA-Protein Interaction Analysis (ChIP-Seq) , that can accurately survey interactions between protein, DNA, and RNA to interpret regulation events central to many biological processes and disease states. Quantify in vivo protein-DNA interactions using the combination of chromatin immunoprecipitation with Illumina's sequencing technology (ChIP-Seq) on a genome-wide scale.

Therefore, through implementation of the various modules of the Illumina platform it is possible perform genomics and transcriptomics studies of any type, even in veterinary and agronomic fields where Illumina technology is getting, in recent months, surprising results, leading, for example, to the definition of three-dimensional model of the yeast genome or revealing, by means of high-resolution sequencing of mRNA, the complexity of the grown rice transcriptome  much larger than was believed until now.

The Research Unit is coordinated by Prof. F.P. Schena, ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). The facility is managed by Dr. F. Sallustio, University of Bari, ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )  and is allocated at the CARSO Consortium, Valenzano (Bari), Italy.

PRICE LIST

 

Gene Expression FFPE Service

Service Price

 

Sample processing

Includes:

- Microarray Slide

- Reagents

- Quality control of total RNA samples (Agilent 2100 Bioanalyzer) (1 h.)

- Generation of labeled cRNA (48 h. con varie fasi di incubazione)

- Quality control of labeled cRNA samples (0.5 h) (Nanodrop)

- Microarray hybridization (24 h.)

 - Washing and Scanning (3 h.)

- Raw data generation (TIFF image) (30’)

- Raw data processing with Genome Studio (15’/sample)

430,00 € per sample

Data analysis (8 h)

Includes:

- Normalization (GeneSpring GX)

- Statistics and data quality control

- Analysis of differentially expressed genes

- Analysis of relevant biological processes and pathways (GeneSpring GX)

- Data transfer

- Comprehensive report

500,00 € per project and per pair wise comparison

   

 

Genotyping/CNV Service (with CytoSnp microarray)

Service Price

Sample processing

Includes:

- Microarray Slide

- Reagents

- Quality control of genomic DNA samples (agarose ge, 2h.)

- DNA amplification (24 h.)

- Fragmentation- Precipitation (4 h.)

- Microarray hybridization (24 h)

 -Washing and Scanning (3 h.)

- Raw data generation (TIFF image) (30’)

- Raw data processing with Genome Studio (15’/sample)

330,00 € per sample

   

Data analysis (8 h)

Includes:

Includes:

- Statistics and data quality control

- Measurement of DNA copy number changes (Genome studio)

- Data transfer

- Comprehensive report

500,00 € per project and per pair wise comparison

THE TRANSCRIPTOMIC AGILENT FACILITY 

  

Core facility description:

ñ Agilent High Resolution C Scanner: Agilent Technologies microarray scanner suitable for gene expression profiling, microRNA expression profiling, genome micro and macro deletion and/or duplication identification (array-based CGH), protein and/or transcription factor binding sites identification (ChIP-on-chip) and for active and inactive gene identification in the genome (methylation assays).  Compatible with standard 1”x3” (25 mm x 75 mm) glass slides available for samples extracted from human and several animal and plant model organisms cells and tissues.

ñ Microarray Hybridization Oven for optimal microarray hybridization performance.

ñ HP xw4600 Workstation for the appropriate microarray data analysis.

 

Expertise and services for Institutions and Industries:

ñ Gene expression analysis: identification of differentially expressed genes between two or more conditions, starting from total RNA extracted from human, plant and animal cells and tissues.

ñ microRNA expression analysis: identification of differentially expressed microRNAs between two or more conditions, starting from total RNA extracted from human, plant and animal cells and tissues.

ñ ChIP-on-chip service: identification of protein and/or transcription factors DNA binding sites, starting from genomic DNA extracted from human, plant and animal cells and tissues, previously immuno-precipitated with the protein of interest.

ñ Methylation assay service: identification of active and inactive genes in the genome, starting from genomic DNA extracted from human, plant and animal cells and tissues.

ñ Array-based CGH service:  identification of micro and macro deletions and/or duplications in the genome, starting from genomic DNA extracted from human, plant and animal cells and tissues.

 

 

The Research Unit is coordinated by Prof. L. Gesualdo ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). The facility is managed by Dr. Acetturo, University of Bari, ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it )  and is allocated at the Renal Unit, Policlinico, Bari, Italy.

PRICE LIST

Gene Expression Service

Service Price

Setup costs

Includes:

- Microarray Slide

- Appropriate Gasket-Slide

See Agilent purchase prices

Sample processing

Includes:

- Quality control of total RNA samples (Agilent 2100 Bioanalyzer) (4 h)

- Reagents

- Generation of labeled cRNA (10 h)

- Quality control of labeled cRNA samples (Nanodrop) (30’)

- Microarray hybridization (20 h)

- Washing and Scanning (2 h)

- Raw data generation (TIFF image) (30’)

- Raw data processing with Feature Extraction (15’/sample) 

170,00 € per sample

Data analysis (8 h)

Includes:

- Normalization (GeneSpring GX)

- Statistics and data quality control

- Analysis of differentially expressed genes

- Analysis of relevant biological processes and pathways (GeneSpring GX)

- Data transfer

- Comprehensive report

500,00 € per project and per pair wise comparison

 

ChIP-on-chip Service

Service Price

Setup costs

Includes:

- Microarray Slide

- Appropriate Gasket-Slide

See Agilent purchase prices

Sample processing

Includes:

- Labeling of genomic IP DNA (5 h)

- Reagents

- Purification of labeled genomic DNA (1 h)

- Microarray hybridization (40 h)

- Washing and Scanning (2 h)

- Raw data generation (TIFF image) (30’)

- Raw data processing with Feature Extraction (15’/sample) 

220,00 € per sample

Data analysis (8 h)

Includes:

- Normalization (Agilent Genomic Workbench)

- Statistics and data quality control

- Information extraction (Agilent Genomic Workbench

- Data transfer

- Comprehensive report

500,00 € per project and per pair wise comparison

 

Methylation Service

Service Price

Setup costs

Includes:

- Microarray Slide

- Appropriate Gasket-Slide

See Agilent purchase prices

Sample processing

Includes:

- Reagents

- Sample preparation (35 h)

- Sample labeling (4 h)

- Purification and determination of yield, degree of labeling or specific activity (Nanodrop) (1 h)

- Microarray hybridization (42 h)

- Washing and Scanning (2 h)

- Raw data generation (TIFF image) (30’)

- Raw data processing with Feature Extraction (15’/sample) 

220,00 € per sample

Data analysis (8 h)

Includes:

- Normalization (Agilent Genomic Workbench)

- Statistics and data quality control

- Information extraction (Agilent Genomic Workbench

- Data transfer

- Comprehensive report

500,00 € per project and per pair wise comparison

 

aCGH Service

Service Price

Setup costs

Includes:

- Microarray Slide

- Appropriate Gasket-Slide

See Agilent purchase prices

Sample processing

Includes:

- gDNA Quantitation and Quality Analysis (Nanodrop) (30’)

- Reagents

- Sample preparation (5 h – 7 h)

- Sample labeling (3 h)

- Purification and determination of yield, degree of labeling or specific activity (Nanodrop) (1,5 h)

- Microarray hybridization (26 h – 42 h)

- Washing and Scanning (2 h)

- Raw data generation (TIFF image) (30’)

- Raw data processing with Feature Extraction (15’/sample) 

220,00 € per sample

Data analysis (8 h)

Includes:

- Statistics and data quality control

- measurement of DNA copy number changes (Agilent Genomic Workbench)

- Data transfer

- Comprehensive report

500,00 € per project and per pair wise comparison

 

Slide scanning and Feature Extraction Service

Service Price

1 x 3" (25 mm x 75 mm) glass slide scanning

70 € per slide

Feature extraction

30 € per slide

 

Agilent slide prices

 

Arrays for GENE EXPRESSION

Cod. N.

Slides/Kit

Arrays/Slide

Description

Price (€)

G4502A

1

1

1 X 244K

487

G4503A

1

2

2 X 105K

635

G2514F

1

4

4 X 44K

741

G2509F

1

8

8 X 15K

847

G4860A

1

1

1 X 1M

588

G4861A

1

2

2 X 400K

758

G4862A

1

4

4 X 180K

889

G4102A

1

8

8 X 60K

1012 

 

Arrays for miRNA

Cod. N.

Slides/Kit

Arrays/Slide

Description

Price (€)

G4474A

1

8

8 X 15K

1354

 

Arrays for CGH

Cod. N.

Slides/Kit

Arrays/Slide

Description

Price (€)

G4423A

1

1

1 X 244K

487

G4425A

1

2

2 X 105K

640

G4426A

1

4

4 X 44K

741

G4427A

1

8

8 X 15K

847

G4123A

1

1

1 X 1M

588

G4124A

1

2

2 X 400K

758

G4125A

1

4

4 X 180K

889

G4126A

1

8

8 X 60K

1012

 

Arrays for ChIP-on-chip and DNA Methylation

Cod. N.

Slides/Kit

Arrays/Slide

Description

Price (€)

G4496A

1

1

1 X 244K

487

G4498A

1

2

2 X 105K

635

G4497A

1

4

4 X 44K

741

G4499A

1

8

8 X 15K

847

G4819A

1

1

1 X 1M

588

G4820A

1

2

2 X 400K

758

G4821A

1

4

4 X 180K

889

G4822A

1

8

8 X 60K

1012

 

THE PROTEOMIC BRUKER DALTONICS FACILITY

Core facility description

 

The core facility includes: 1) a complete bidimensional electrophoresis apparatus (2D-PAGE) equipped with an imaging analysis system ("PROXPRESS 2D"-Perkin Elmer); an automated protein digestion workstation (Proteineer dp e fc, Bruker Daltonics); several mass spectrometers useful for protein identification, sequencing and characterization of post translational modifications (Autoflex III, and HCTultra™ ETD II, Bruker Daltonics ) as well as for the identification of disease related protein expression profiles (SELDI-TOF/MS, Bio-Rad). Moreover, recent acquisition of a license for the use of LUCID® technology (Bruker Daltonics/Bio-Rad) offers an innovative approach for the analysis of SELDI proteinChips by MALDI-TOF-TOF/MS/MS which could allow direct sequencing of SELDI differently expressed mass peaks. This combined approach can lead to a short-term identification of new biomarkers useful both for diagnosis of human and animal diseases and for improving food safety and traceability.

 

Expertise and services for Institution and Industries.

Characterization of the whole protein expression (proteome) in human, animal and vegetable biological samples. One of the main aims of the laboratory is the identification of protein markers associated to pathological or physiological state in both medical and agronomic field.

In the medical field, the focus of the research activity is the identification, mainly in biological samples, of disease biomarkers useful for both early diagnosis and monitoring of the progression of organ damage. Applicative examples are the screening of the urine proteome with the aim of recognizing non invasive biomarkers for the diagnosis and the prognosis of renal diseases such as IgA Nephropathy (Rocchetti et al. proteomics 2008) or Diabetic Nephropathy (Papale et al. Diabetes Care, 2010) and the analysis of the plasma proteome for the identification of Renal Cell Carcinoma and Colon Cancer biomarkers.

In the agro-food field, the current research activity is mainly focused on the characterization of the typical food and food safety. Some of the research interests the proteomic differential analysis of corn cultivars either at basal state and after stress induction; the proteomic characterization of cherry and lentil cultivars and the identification of grape-cultivars biomarkers (Papale et. al Am. J. of Enology and Viticulture 2010).

 

Services for Biomedical field

  • SELDI-TOF/MS and/or MALDI-TOF-TOF/MS profiling for the identification, in biological fluids such urine, saliva and serum/plasma, of protein biomarkers useful for early diagnosis, differential diagnosis and prognosis of both systemic and organ-specific diseases. 
  • MALDI-TOF/TOF-MS analysis of candidate biomarkers to obtain protein identification by both Peptide Mass Fingerprinting (PMF) and protein sequencing (MS/MS).

 

Services for Agro-food field

  • SELDI-TOF/MS and/or MALDI-TOF-TOF/MS profiling for the identification of protein biomarkers useful for food traceability and safety.
  • MALDI-TOF/TOF-MS analysis of candidate cultivar-specific biomarkers by Peptide Mass Fingerprinting (PMF) and protein sequencing (MS/MS).
  •  
  • The research Unit is coordinated by Prof. Elena Ranieri ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). The core facility is managed by Dr. Massimo Papale ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it or This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) and is allocated at the Research Centre “Bioagromed” at the University of Foggia, Italy.

PRICE LIST

________________________________________________________________________________

Proteomic service

Cost (in Euro, VAT not included) 

Sample processing

It includes:

  • Samples fractionation (only for serum/plasma samples)
  • Calibration and quality Control ( SELDI-TOF/MS )
  • SELDI profiling (minimun 4 samples in duplicate) by one ProteinChip type among CM10(basic proteins); Q10 (acidic proteins); H50 (idrophobic proteins) or IMAC (metal binding proteins)
  • Purification of 1 SELDI mass peak and identification by LUCID ID system on   MALDI-TOF-TOF/MS
  • In gel or in solution trypsin digestion
  • MALDI-TOF-TOF/MS analysis of a protein mixture

 

 

  • 70

 

  • 60

 

  • 300 
  • 1000

 

  • 80
  • 120

This analysis include the following activities:

-For low molecular weight (< 4 kDa) pepetides: Sample concentration; chromatographic fractionation of the sample to enrich the interested mass peak; SELDI analysis of all the chromatographic fractions to identify that containing the enriched marker; sequencing of the interested mass peak by MALDI-TOF-TOF/MS

- For proteins and peptides higher then 4 kDa: Sample concentration; chromatographic fractionation of the sample to enrich the interested mass peak; SELDI analysis of all the chromatographic fractions to identify that containing the enriched marker; separation of the enriched chromatographic fraction by mono-dimensional or two-dimensional electrophoresis; pick-up of the interested gel spot; SELDI-TOF/MS analysis to check the correspondence between the mass peak and protein eluted from gel spot; in-gel trypsin digestion and analysis by  MALDI-TOF-TOF/MS (both PMF and sequencing)

THE METABOLOMIC BRUKER BIOSPIN FACILITY 

 

Core facility description

The technological equipment of the Metabolomics platform consists of a Bruker Avance AV 500 WB spectrometer (by Bruker BioSpin S.r.l), equipped with a cryomagnet of 11.7 Tesla (1H frequency = 500 MHz). The instrument is equipped with a TBI probe and other direct and inverse multinuclear probes, and a unit gradient GREAT 1/10 type. The acquisition system PC Linux on the workstation is complete of the appropriate software Topspin 1.3 (by Bruker Biospin), added of data transfer system via Filezilla (FTP) and SSH software Bruker AMIX, with particular focus on multivariate statistical analysis of spectra of mixtures.

Expertise and services for Institutions and industries

 

High-resolution nuclear magnetic resonance spectrometer (Avance 500 NMR) can take measurements on various samples. The potential applications of the technology include:

-analysis of small organic molecules;

-quality-controls;

-analysis of food (oil, wine, meat, etc.);

-analysis of body fluids (serum, cerebrospinal fluid, urine, etc.);

-metabolomics.

 

The Metabolomics Research Unit is coordinated by Prof. FP Fanizzi ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). The platform is managed by Dr.ssa L. Del Coco ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ; This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).

 

 

PRICE LIST

 

Nuclear Magnetic Resonance Service- Bruker Avance DRX  500 MHz

Service Price

Setup costs

Includes:

- NMR Deuterated Solvents

- NMR tubes

- NMR Reference Standards

- Laboratory glassware

- Cryogenic Liquids. Liquid Nitrogen and liquid Helium

 

150,00 €

Data acquisition

Includes:

-Analysis of proton (1H-NMR) spectrum of standard (Including printable data with expansions, indicating chemical shift of the peaks, integration, supply data file) (20’)

-Variations on the 1D experiment include:

Carbon and Heteronuclear NMR spectra:

-1D Carbon experiment (Including printable data with expansions, indicating chemical shift of the peaks, integration, supply data file) (8h)

- 2D COSY - Proton-proton correlation experiment (5h)

-NOESY - Proton-proton through-space interactions via NOE (8h)

(Including printable data with expansions, indicating chemical shift of the peaks, integration, supply data file) (6h)

-HETCOR - Proton-Carbon correlation experiment (6h)

(Including printable data with expansions, indicating chemical shift of the peaks, integration, supply data file)

 

 

100,00 €

 

 

 250,00 €

 

 

 

 

 

 

 

 250,00 €

Data analysis (8 h)

Includes:

- Processing NMR data

- Statistical analysis

- Software Amix (Bruker Biospin)

- Data transfer

- Comprehensive report

 

 

250,00 € per sample

    

THE SYSTEMS BIOLOGY LABORATORY

 

Core facility description:

The Systems Biology Laboratory locating in the Istituto di Studi sui Sistemi Intelligenti per l’Automazione - CNR in Bari is involved since several years in national and international projects and collaborations. It has as main objective the building of in silico models for the study of complex and multi-factorial pathologies such as the cancer. The multi-disciplinary group, composed by physicists, computer scientists and biotechnologists, is characterized by its capability to analyze and to integrate multidimensional data provided by the high-throughput platforms now available. Genomics, transcriptomics, proteomics and metabolomics help to study gene–environment interactions and to identify the factors that determine the pathology onset and progression by analyzing data on an enormous variety of molecules involved in the biological processes (DNA, mRNA, proteins, lipids, metabolites). Our challenge is to integrate the different types of data in a global model able to reveal the molecular mechanisms underlying particular pathologies and to predict new therapeutic strategies. 

 

Expertise and services for Institutions and Industries:

  • HIGH-THROUGHPUT DATA ANALYSIS AND INTEGRATION
    • Identification of markers associated with the phenotypic conditions in analysis by applying parametric and non parametric univariate statistics on patient specific data provided by the high-throughput platforms of genomics, transcriptomics, proteomics and metabolomics.
    • Classification of different phenotypes by using techniques of multivariate statistics analysis to process high-throughput data that involve a number of biomarkers larger than the number of  available observations.
    • Prediction of the phenotypic status of a patient  by analyzing a set of multi-dimensional data collected by high-throughput platforms on patient and controls groups. In particular, we developed techniques of supervisioned learning of a model of prediction/classification for the omics data. These techniques based on a strategy of regularization allow the processing of large dimension and small sample size data  and ,unlike the univariate methods, they are able to take into account the patterns of interaction of multivariate biomarker datasets. Once the model in silico has been obtained, the user will be able to predict the phenotype by using genomics, transcriptomics, proteomics and metabolomic patient specific data.
    • Integration of different types data for a systemic study of multi-factorial pathologies by using multi-task regularized methods.

 

 

  • PATHWAY ANALYSIS ON HIGH-THROUGHPUT DATA

Identification of significant biologically patterns in high-throughput data related  to two different phenotypic conditions: a gene enrichment analysis of Gene Ontology categories, pathways or user-defined biomarker lists by Random Set Methods e Gene List Analysis with Prediction Accuracy (GLAPA).

 

  • STUDY OF BIOLOGICAL NETWORKS

Methods to infer large scale networks by using probabilistic  graphical models (Gaussian Graphical Models)  based on estimates of the conditional dependencies between biomarkers. The method uses regularized linear regression for estimating the partial correlation coefficients between the variables.

 

 

The Systems Biology Laboratory is coordinated by Dr. N. Ancona ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) and the facility is managed by  Dr. T. M. Creanza ( This e-mail address is being protected from spambots. You need JavaScript enabled to view it This e-mail address is being protected from spambots. You need JavaScript enabled to view it ).

 

 

 

 Service cost

The services cost will be determined by quantifying the required man power and competences.