Services

At present, the services offered by the Microarray Facility at DMSD-Unife allows the analysis of messenger RNAs or microRNAs or UCRs expression in biological samples from various mammalian species or other animal and vegetable species 5.

From the offered services, the client can obtain: (1) microarray "raw data" of quantified genes, ready for further biostatistic and bioinformatic analyses; (2) biostatistic and bioinformatic analyses to acquire information of biological significance from microarray "raw data".

More specifically, the various types of services are as follows:

  • Agilent microRNA microarray (human, mouse, ...)
  • Agilent Gene expression microarrays (human, mouse, ...)
  • UCR (Ultraconserved region) Microarray
  • RNA quality assessment (Nanodrop, Bioanalyzer...)
  • Analisi bioinformatiche (GeneSpring GX software, BRB-ArrayTools, SAM, PAM and many others)
  • Custom microarray development (based on Agilent platform)

Unique in Italy, the Microarray Facility has been recently accredited as an "Agilent Service Provider" for microRNA expression analyses.
 

Code
Service feature

FULL ANALYSES: mRNA, microRNA and UCR Expression
1001
Expression Analysis (one color) whole genome on Agilent platform (human, mouse, rat genome; consult the service for other species)

INCLUDED:
(i) RNA quality and quantity control
(ii) RNA fluorescent labeling and labelled RNA quality control
(iii) hybridization on array
(iv) image acquisition and fluorescent signal quantification
(v) raw data delivery by web, email or storage device (CD, DVD))

NOT INCLUDED:
(i) data analysis
(ii) data submission on public databases

Required: 2 ug RNA (about 200 ng/ul). Invitrogen Trizol (cat. 15596-026) or similar is the preferred method for RNA purification Please, contact Facility for other compatible methods.

1002
Gene Expression Analysis on user array

(NOTE: IT IS NECESSARY TO CONTACT THE FACILITY TO VERIFY IF ARRAY IS COMPATIBLE WITH OUR PLATFORM !!! )

INCLUDED:
(i) RNA quality and quantity control
(ii) RNA fluorescent labeling and labeling quality control (IF compatible with our procedures)
(iii) hybridization on array
(iv) image acquisition and fluorescent signal quantification
(v) raw data delivery by web, email or storage device (CD, DVD))

NOT INCLUDED:
(i) data analysis
(ii) data submission on public databases

Required: Microarray, array printing design, array GAL file and all the available array information (description file, manufacturing, company...) and 2 ug RNA (about 200 ng/ul). Invitrogen Trizol (cat. 15596-026) or similar is the preferred method for RNA purification. Please, contact Facility for other compatible methods.


Other services

Code
PARTIAL ANALYSIS
1011
Qualitative analysis of RNA with Bioanalyzer
1012
Quantitative analysis of RNA with Nanodrop
1021
Scanning microarray chip and data acquisition (the client provides the microarray chip ready for being scanned)
1031
Data maintenance (images and quantifications) for 1 year.
NOTE: data are normally kept at the Facility for 1 months from the end of service and are removed to recover disk space.

Biostatistic and bioinformatic analyses

In addition to the laboratory experiments, we also provide support for data analyses. Although client will be responsible for the final experimental design, we may also provide help with preliminary experimental design.

Code
BIOINFORMATIC ANALYSES

Pre-experimental consultation to define the best experimental setting, to answer statistical issues and to evaluate the experimental costs
2001
Evaluation of samples quality by using GeneSpring GX and experiment set-up
2002
Data analysis to identify genes differentially expressed among two or more classes (e.g treated vs. untreted, cancer vs. normal). The service includes:

a. Quality control, normalization, summarization
b. Fold-change analysis
c. Parametric tests (t-Test, ANOVA, ...)
d. Non-parametric tests (Mann-Whitney, Wilcoxon, Rank Products, ...)

2003
Customized analyses (to be defined in accordance to client needs and aims):

a. Class comparison
b. Supervised and unsupervised clustering
c. Principal Component Analysis
d. Prediction analysis
e. Gene set enrichment analysis
f. Pathway enrichment analysis
g. Gene Ontology analysis
h. Publication support (methods, figures, tables)


Other bioinformatic services

2011
Preparation of MIAME-compliant microarray data for submission to public databases (ArrayExpress or GEO)
2012
Submission of MIAME-compliant microarray data to public databases (ArrayExpress or GEO)