Industrial Research and Technology Transfer Laboratory accredited by Emilia Romagna Region (DGR 1213/2007) with Deliberation n.GPG/2012/119 of February 6, 2012.
Industrial Research and Technology Transfer Laboratory accredited by Emilia Romagna Region (DGR 1213/2007) with Deliberation n.GPG/2012/119 of February 6, 2012.
LTTA Microarray Facility is a laboratory certified by Agilent Technologies and it is classified as a Certified Service Provider (https://www.genomics.agilent.com). A DNA microarray represents a technological platform able to detect and quantify thousands of nucleotide sequences at the same time. The technology, developed in the field of bio-medical research, has been mainly used to simultaneously examine the expression of thousands of genes or to detect the presence of genetic sequences of microbial pathogens (viruses, bacteria). However, it can also find application in fields, such as veterinary, agriculture, environment monitoring. The approach can be used for the high-throughput detection of micro-organisms in water and food.
A DNA microarray is made of an ordered grid of DNA probes linked to a solid surface, about few centimetre square in size. On this surface thousands or hundreds of thousands of probes able to detect the same number of genetic elements can be physically linked 3. If the specific probe is present on the microarray, then the biological element can be detected based on the sequence homology between nucleic acids (DNA or RNA). In other words, the intrinsic genetic characteristic of the biological element is used for its detection.
Microarray technology employs an inverse hybridization approach: it is the sample's nucleic acid (DNA or RNA) that is labelled (with a fluorochrome) instead of the probes. Then, the complex mixture of genetic elements that are present in each sample are allowed to hybridize (anneal to the specific probe on the basis of sequence homology). Based on its sequence homology, each microarray probe hybridizes to the homologous elements among the thousands that are present in each sample and allows the quantification of each one of them. Thus, this techniques allows the simultaneous detection and quantification of thousands of genetic elements.
In our facility’s laboratories, instruments for the overall analysis of Agilent microarrays are available. It will be possible not only to use human mRNAs, microRNAs and UCRs microarrays, but also other animal and vegetal species. All commercially available Agilent microarrays can be used. Our staff have many years’ experience in microarray hybridisation and data analysis, as may be seen by the many scientific publications in the field.
In addition, it is possible to develop customized microarrays. All microarrays, including "custom", are developed with the "ink-jet" Agilent technology. Microarrays are not produced at LTTA Microarray Facility, but at Agilent, which guarantees quality and reproducibility of the microarrays over time. If commercially available, the client can eventually choose to buy the microarray directly from Agilent.
We offer free pre-experimental consultation to ensure your study to be solid, scientifically worthwhile and as economical as possible. We give advice in experimental design questions and statistical issues.
We offer statistical and bioinformatic data analysis on primary data and downstream functional analyses that include significant genes identification, class prediction. We support data from our and other, outside, platforms; and can help with publication and database submission. Our software packages include GeneSpring GX Analysis Platform comprehensive of Pathway analysis module, BRB-ArrayTools, SAM (Significance Analysis of Microarrays), PAM (Prediction Analysis of Microarrays).
All data generated from the facility are stored in a confidential database and are accessible through a ftp server. Data and information supplied by the facility are intended for research use only.
The microarray facility provides analyses of gene expression (mRNA, microRNA, ultraconserved regions) based on the Agilent platform.
In addition to the microarrays already available, custom microarrays can be developed to meet clients’ needs.
Our staff has a wealth of experience in microRNA expression profile analysis, a rapidly expanding area of research, with many potential applications.
The facility has developed an innovative microarray for analysing ultraconserved regions (UCRs).
At present, the services offered by the Microarray Facility allows the analysis of messenger RNAs or microRNAs or UCRs expression in biological samples from various mammalian species or other animal and vegetable species.
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:
Unique in Italy, the Microarray Facility has been recently accredited as an "Agilent Service Provider" for microRNA expression analyses.
High-Resolution Microarray Scanner
The Agilent High-Resolution C scanner can perform high-density microarray analysis (to a resolution of 2μ). Optimised through SureScan High Resolution Technology, the dynamic range is now 20 times greater than other leading scanners. Seamless data processing and the dynamic autofocus (the first of its kind) help deliver clarity and quality in research.
NanoDrop 1000 (Thermo Scientific)
A UV spectrophotometer for microvolume quantification of nucleic acid or proteins.
2100 Bioanalyzer (Agilent Technologies)
This is a microfluidics-based platform for extremely rapid sizing, quantification and quality control of DNA, RNA, proteins and cells.
GeneSpring GX
GeneSpring software, from Agilent Technologies, provides the ideal instrument for the visualisation and analysis of microarray experiments. It is an ideal graphic environment for the design, analysis and management of key applications for microarray.
Data extraction software
Agilent Feature Extraction software reads and processes up to 100 microarray image files in an automated mode. The software automatically finds and places the grids, classifies and selects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels and calculates statistical confidences.
Bioinformatics
Open-source software for statistical and bioinformatics analysis. The following open-source software is used: R, BRB Array tools, Cluster 3.0, Java Treeview, yEd graph Editor, Weka 3.6.3, BWA, Samtools, gAtk and GAMES.
Microarray Facility
Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA)
Area Polo Chimico Biomedico 'CUBO' – second floor
Via Fossato di Mortara, 70 - 44121 Ferrara
Prof. Massimo Negrini
ngm@unife.it
+39 0532 455399
Dr Cristian Bassi
bsscst@unife.it
+39 0532 455393
Dr Cristian Bassi
Dr Paola Guerriero
Dr Silvia Sabbioni
| Rigolin, G.M., E. Saccenti, A. Melandri, M. Cavallari, A. Urso, F. Rotondo, A. Betulla, L. Tognolo, M.A. Bardi, M. Rossini, E. Tammiso, C. Bassi, F. Cavazzini, M. Negrini, and A. Cuneo, In chronic lymphocytic leukaemia, SLAMF1 deregulation is associated with genomic complexity and independently predicts a worse outcome. Br J Haematol, 2020. DOI: 10.1111/bjh.16865. PubMed |
| Roncarati, R., L. Lupini, E. Miotto, E. Saccenti, S. Mascetti, L. Morandi, C. Bassi, D. Rasio, E. Callegari, V. Conti, R. Rinaldi, G. Lanza, R. Gafa, A. Papi, A. Frassoldati, S. Sabbioni, F. Ravenna, G.L. Casoni, and M. Negrini, Molecular testing on bronchial washings for the diagnosis and predictive assessment of lung cancer. Mol Oncol, 2020. 14(9): p. 2163-2175. DOI: 10.1002/1878-0261.12713. PubMed |
| Mensa, E., M. Guescini, A. Giuliani, M.G. Bacalini, D. Ramini, G. Corleone, M. Ferracin, G. Fulgenzi, L. Graciotti, F. Prattichizzo, L. Sorci, M. Battistelli, V. Monsurro, A.R. Bonfigli, M. Cardelli, R. Recchioni, F. Marcheselli, S. Latini, S. Maggio, M. Fanelli, S. Amatori, G. Storci, A. Ceriello, V. Stocchi, M. De Luca, L. Magnani, M.R. Rippo, A.D. Procopio, C. Sala, I. Budimir, C. Bassi, M. Negrini, P. Garagnani, C. Franceschi, J. Sabbatinelli, M. Bonafe, and F. Olivieri, Small extracellular vesicles deliver miR-21 and miR-217 as pro-senescence effectors to endothelial cells. J Extracell Vesicles, 2020. 9(1): p. 1725285. DOI: 10.1080/20013078.2020.1725285. PubMed |
| Gramantieri, L., D. Pollutri, M. Gagliardi, C. Giovannini, S. Quarta, M. Ferracin, A. Casadei-Gardini, E. Callegari, S. De Carolis, S. Marinelli, F. Benevento, F. Vasuri, M. Ravaioli, M. Cescon, F. Piscaglia, M. Negrini, L. Bolondi, and F. Fornari, MiR-30e-3p Influences Tumor Phenotype through MDM2/TP53 Axis and Predicts Sorafenib Resistance in Hepatocellular Carcinoma. Cancer Res, 2020. 80(8): p. 1720-1734. DOI: 10.1158/0008-5472.CAN-19-0472. PubMed |
| Fornari, F., L. Gramantieri, E. Callegari, R.C. Shankaraiah, F. Piscaglia, M. Negrini, and C. Giovannini, MicroRNAs in Animal Models of HCC. Cancers (Basel), 2019. 11(12). DOI: 10.3390/cancers11121906. PubMed |
| Cinausero, M., N. Laprovitera, G. De Maglio, L. Gerratana, M. Riefolo, M. Macerelli, M. Fiorentino, E. Porcellini, V. Buoro, F. Gelsomino, A. Squadrilli, G. Fasola, M. Negrini, M. Tiseo, M. Ferracin, and A. Ardizzoni, KRAS and ERBB-family genetic alterations affect response to PD-1 inhibitors in metastatic nonsquamous NSCLC. Ther Adv Med Oncol, 2019. 11: p. 1758835919885540. DOI: 10.1177/1758835919885540. PubMed |
| Ramassone, A., A. D'Argenio, A. Veronese, A. Basti, S.H.A. Soliman, S. Volinia, C. Bassi, S. Pagotto, M. Ferracin, L. Lupini, E. Saccenti, V. Balatti, F. Pepe, L.Z. Rassenti, I. Innocenti, F. Autore, L. Marzetti, R. Mariani-Costantini, T.J. Kipps, M. Negrini, L. Laurenti, and R. Visone, Genetic dynamics in untreated CLL patients with either stable or progressive disease: a longitudinal study. J Hematol Oncol, 2019. 12(1): p. 114. DOI: 10.1186/s13045-019-0802-x. PubMed |
| Shankaraiah, R.C., L. Gramantieri, F. Fornari, S. Sabbioni, E. Callegari, and M. Negrini, Animal Models of Hepatocellular Carcinoma Prevention. Cancers (Basel), 2019. 11(11). DOI: 10.3390/cancers11111792. PubMed |
| Roncarati, R., L. Lupini, R.C. Shankaraiah, and M. Negrini, The Importance of microRNAs in RAS Oncogenic Activation in Human Cancer. Front Oncol, 2019. 9: p. 988. DOI: 10.3389/fonc.2019.00988. PubMed |
| Quaglia, F.M., G.M. Rigolin, E. Saccenti, M. Negrini, E. Volta, M. Dabusti, M. Ciccone, A. Urso, M. Laudisi, and A. Cuneo, Response to Ibrutinib of a Refractory IgA Lymphoplasmacytic Lymphoma Carrying the MYD88 L265P Gene Mutation. Mediterr J Hematol Infect Dis, 2019. 11(1): p. e2019057. DOI: 10.4084/MJHID.2019.057. PubMed |
Centralised Service for transcriptome analysis of biological samples using an Agilent-based microarray system and bioinformatics analysis
At LTTA we have a transcriptome analysis service using microarray (Agilent platform) and a bioinformatics analysis service.
The service can highlight the levels of expression of messenger RNA or microRNA or ultraconserved regions (UCRs) in biological samples of different species.
Using the service, users can obtain (1) quantification of the expression of the genes present in the genome under examination in the form of raw data, ready for analysis using bioinformatics approaches; (2) bioinformatics analysis to obtain information on the biological significance of the microarray data; (3) bioinformatics analysis of gene expression data, last generation sequencing, CGH, SNP, CNV supplied by the user.
The different types of service and relevant costs are shown below.
1. Quantification using microarray for gene expression in a tested genome
Our Service offers:
| Code no. | Type of service | Cost per sample (€) |
| COMPLETE ANALYSIS | ||
| B1001 | Gene Expression Analysis (1 colour) for the entire genome on Agilent microarray platform (human, mouse or rat; please ask the Service about other species) The complete service includes: (i) qualitative and quantitative RNA analysis using Bioanalyzer (ii) RNA sample marking using fluorescent probe (iii) hybridisation of labelled sample on chip (iv) chip scan and data acquisition (v) sending raw data by computer (downloading via web or DVD) (vi) description of the procedure for scientific publishing purposes The complete service does not include: (i) data analysis (ii) submission of data to public databases Users are kindly requested to provide: 2 μg RNA at a concentration no lower than 200 ng/μl (Purification using Trizol Invitrogen produces RNA of a suitable quality for performing investigations) |
538.50 |
| B1002 | Gene Expression Analysis on user-supplied microarray (PLEASE NOTE: YOU MUST CONTACT THE SERVICE IN ADVANCE TO CHECK WHETHER THE USE OF MICROCHIPS PRODUCED BY COMPANIES OTHER THAN AGILENT!!!) Apart from supplying the slide containing the array, the service includes all the stages described previously (Type 1a), i.e.: (i) qualitative and quantitative RNA analysis using Bioanalyzer (ii) RNA sample marking using fluorescent probe (iii) hybridisation of labelled sample on chip (iv chip scan and data acquisition (v) sending raw data by computer (downloading via web or DVD) (vi) description of the procedure for scientific publishing purposes The service does not include: (i) bioinformatic data analysis (ii) submission of data to public databases Users are requested the slide containing the array supplied with a suitable file for recognising the samples on the grid (e.g. GAL file) and 2 μg RNA at a concentration of 200 ng/μl (Purification using Trizol Invitrogen produces RNA of a suitable quality for performing investigations) |
323.10 |
Other services:
| Code no. | PARTIAL ANALYSIS | Cost per sample (€) |
| B1011 | RNA qualitative and quantitative analysis using Bioanalyzer (multiples of 12 samples) | 32.30 (per 1-12 samples) |
| B1021 | chip scan and data acquisition (user supplies the hybridised slide to be scanned) | 21.10 |
| B1031 | Data storage (images and quantifications) for 1 year in dedicated hard drive. N.B.: data are stored on the Service’s computer for 1 month. After this time, the data will be deleted to recover space on the hard disk. |
5.40 |
2. Agilent microarray bioinformatics analysis
In addition to the service above, it is possible to obtain support for data analysis.
| Code no. | DESCRIPTION | Cost (€) |
| Preliminary consultation for setting up the experimental design during which time an estimate of the overall cost of the analyses requested can be made | No charge | |
| B2001 | Setting-up of experiment: entering data for analysis using GeneSpring software (transcriptome software) | 5.40/sample |
| B2002 | Data analysis to identify genes differentially expressed between two classes (for example: treated vs. non-treated samples, or cancer vs. normal samples). The service includes:
|
161.60 |
| B2003 | Custom analyses by arrangement. This type of service requires active contribution from the user on hypotheses about the experiment in order to define the type of analysis to be performed. For example:
|
86.10/hour |
3. Bioinformatics analysis
| Code no. | BIOINFORMATICS ANALYSIS | Cost (€) |
| B3001 | Basic microarray experiment analysis: an experiment is understood to mean all the data relating to a biological sample. DAMA will perform the complete analysis of a 2-class experiment (for example, diseased and healthy samples), including quality control. Users will receive the results of the processing, including a list of the genes and significant values. N.B.: The analysis will only be performed once the data relating to all the samples in the experiment have been provided. | 340.50 |
| B3002 | Extended basic analysis to include additional sample data and extend the experiment to 2 classes, as referred to at BIO3001. | 170.30 |
| B3003 | Multivariate analysis: the DAMA analyst will provide a thorough analysis of an experiment involving 2 or more classes (for example, clustering, multidimensional scaling, gene ontology, predictability, chromosome mapping, meta-analysis comparing different experiments, long-term scanning, etc). | 79.50/hour |
| B3004 | MIAME data bank: Submission of experiments to the Database (ArrayExpress or GEO). | 33.30 |
| B3005 | Publication support Graphic processing of results, submission to public databases (EBI and NCBI), online publication of supplementary data, etc). | 90.80/ora |
Some of the services/products offered may be provided with the help of other services of the LTTA Laboratory.
Each service includes a description of the procedure and supply of images of any scientific publication purposes.
Prices are shown without VAT and are subject to change according to the cost of consumables necessary for the service (every 12 months).
We offer statistical and bioinformatics analysis of raw data and downstream functional analysis including significant gene identification, sample classification and gene function analysis. We handle data produced both by our own and by other platforms; we can offer assistance in data publishing and deposition on public databases (GEO ed ARRAYEXPRESS).
Our service also offers analysis of data derived from sequencing. Data are processed and results are presented in form of hypertext, figures, tables or networks.
Open source software is used: PYTHON ,R, BRB-Array tools, Cluster 3.0, Java Treeview, yEd graph Editor, Weka 3.6.3, BWA, Samtools, gAtk, GAMES, and other continuously updated. Web site that can be consulted at: http://aqua.unife.it
Our mission is to offer researchers/clients the possibility of extracting the maximum amount of information from their experiments. We aim to work together with researchers/clients to find the optimal design for their experiments, an essential starting point which is too often overlooked.
Processing of high-throughput genomic data: Next generation sequencing (Illumina, Ion-torrent, SOLiD), Microarray/RT PCR, SNP chips, etc.
Automation of customised bioinformatics procedures.
Open source software for statistical and bioinformatics analysis.
Open source software: PYTHON R, BRB Array tools, Cluster 3.0, Java Treeview, yEd graph Editor, Weka 3.6.3, BWA, Samtools, gAtk and GAMES and other continuously updated.
Bioinformatics
Laboratorio per le Tecnologie delle Terapie Avanzate (LTTA)
Area Polo Chimico Biomedico 'CUBO' – third floor
Via Fossato di Mortara, 70 - 44121 Ferrara
Prof. Stefano Volinia
stefano.volinia@unife.it
+39 0532 455714
Dr Marco Galasso (Ph.D.)
marco.galasso@unife.it
+39 0532 455851
Dr Marco Galasso
Dr Maurizio Previati
| Papaioannou D, Volinia S, Nicolet D, Świerniak M, Petri A, Mrózek K, Bill M, Pepe F, Walker CJ, Walker AE, Carroll AJ, Kohlschmidt J, Eisfeld AK, Powell BL, Uy GL, Kolitz JE, Wang ES, Kauppinen S, Dorrance A, Stone RM, Byrd JC, Bloomfield CD, Garzon R. Clinical and functional significance of circular RNAs in cytogenetically normal AML. Blood Adv. 2020 Jan 28;4(2):239-251. doi:10.1182/bloodadvances.2019000568. PubMed |
| Crudele F, Bianchi N, Reali E, Galasso M, Agnoletto C, Volinia S. The network of non-coding RNAs and their molecular targets in breast cancer. Mol Cancer. 2020 Mar 18;19(1):61. doi: 10.1186/s12943-020-01181-x. PubMed |
| Agnoletto C, Corrà F, Minotti L, Baldassari F, Crudele F, Cook WJJ, Di Leva G, d'Adamo AP, Gasparini P, Volinia S. Heterogeneity in Circulating Tumor Cells: The Relevance of the Stem-Cell Subset. Cancers (Basel). 2019 Apr5;11(4):483.doi:10.3390/cancers11040483. PubMed |
| Galasso M, Morrison C, Minotti L, Corrà F, Zerbinati C, Agnoletto C, Baldassari F, Fassan M, Bartolazzi A, Vecchione A, Nuovo GJ, Di Leva G, D'Atri S, Alvino E, Previati M, Nickoloff BJ, Croce CM, Volinia S. Loss of miR-204 expression is a key event in melanoma. Mol Cancer. 2018 Mar 9;17(1):71. doi:10.1186/s12943-018-0819-8. PubMed |
| Baldassari F, Zerbinati C, Galasso M, Corrà F, Minotti L, Agnoletto C, Previati M, Croce CM, Volinia S. Screen for MicroRNA and Drug Interactions in Breast Cancer Cell Lines Points to miR-126 as a Modulator of CDK4/6 and PIK3CA Inhibitors. Front Genet. 2018 May 18;9:174.doi:10.3389/fgene.2018.00174. eCollection 2018. PubMed |
| Volinia S, Druck T, Paisie CA, Schrock MS, Huebner K. The ubiquitous 'cancer mutational signature' 5 occurs specifically in cancers with deleted FHIT alleles. Oncotarget. 2017 Nov 6;8(60):102199-102211. doi: 10.18632/oncotarget.22321. eCollection 2017 Nov 24.PMID: 29254236 |
| Galasso M, Costantino G, Pasquali L, Minotti L, Baldassari F, Corrà F, Agnoletto C, Volinia S. Profiling of the Predicted Circular RNAs in Ductal In Situ and Invasive Breast Cancer: A Pilot Study. Int J Genomics. 2016;2016:4503840. doi: 10.1155/2016/4503840. Epub 2016 Nov 14. PubMed |
| Garzon R, Volinia S, Papaioannou D, Nicolet D, Kohlschmidt J, Yan PS, Mrózek K, Bucci D, Carroll AJ, Baer MR, Wetzler M, Carter TH, Powell BL, Kolitz JE, Moore JO, Eisfeld AK, Blachly JS, Blum W, Caligiuri MA, Stone RM, Marcucci G, Croce CM, Byrd JC, Bloomfield CD. Expression and prognostic impact of lncRNAs in acute myeloid leukemia. Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):18679-84.doi: 10.1073/pnas.1422050112. Epub 2014 Dec 15. PubMed |
| Volinia S, Nuovo G, Drusco A, Costinean S, Abujarour R, Desponts C, Garofalo M, Baffa R, Aeqilan R, Maharry K, Sana ME, Di Leva G, Gasparini P, Dama P, Marchesini J, Galasso M, Manfrini M, Zerbinati C, Corrà F, Wise T, Wojcik SE, Previati M, Pichiorri F, Zanesi N, Alder H, Palatini J, Huebner KF, Shapiro CL, Negrini M, Vecchione A, Rosenberg AL, Croce CM, Garzon R. Pluripotent stem cell miRNAs and metastasis in invasive breast cancer. J Natl Cancer Inst. 2014 Oct 11;106(12):dju324. doi: 10.1093/jnci/dju324. Print 2014 Dec. PubMed |
| Previati M, Manfrini M, Galasso M, Zerbinati C, Palatini J, Gasparini P, Volinia S. Next generation analysis of breast cancer genomes for precision medicine. Cancer Lett. 2013 Oct 1;339(1):1-7. doi: 10.1016/j.canlet.2013.07.018. Epub 2013 Jul 20. PubMed |
The service works in collaboration with the Department of Mathematics to develop data analysis software.
Centralised Service for transcriptome analysis of biological samples using an Agilent-based microarray system and bioinformatics analysis
At LTTA we have a transcriptome analysis service using microarray (Agilent platform) and a bioinformatics analysis service.
The service can highlight the levels of expression of messenger RNA or microRNA or ultraconserved regions (UCRs) in biological samples of different species.
Using the service, users can obtain (1) quantification of the expression of the genes present in the genome under examination in the form of raw data, ready for analysis using bioinformatics approaches; (2) bioinformatics analysis to obtain information on the biological significance of the microarray data; (3) bioinformatics analysis of gene expression data, last generation sequencing, CGH, SNP, CNV supplied by the user.
The different types of service and relevant costs are shown below.
1. Quantification using microarray for gene expression in a tested genome
Our Service offers:
| Code no. | Type of service | Cost per sample (€) |
| COMPLETE ANALYSIS | ||
| B1001 | Gene Expression Analysis (1 colour) for the entire genome on Agilent microarray platform (human, mouse or rat; please ask the Service about other species) The complete service includes: (i) qualitative and quantitative RNA analysis using Bioanalyzer (ii) RNA sample marking using fluorescent probe (iii) hybridisation of labelled sample on chip (iv) chip scan and data acquisition (v) sending raw data by computer (downloading via web or DVD) (vi) description of the procedure for scientific publishing purposes The complete service does not include: (i) data analysis (ii) submission of data to public databases Users are kindly requested to provide: 2 μg RNA at a concentration no lower than 200 ng/μl (Purification using Trizol Invitrogen produces RNA of a suitable quality for performing investigations) |
538.50 |
| B1002 | Gene Expression Analysis on user-supplied microarray (PLEASE NOTE: YOU MUST CONTACT THE SERVICE IN ADVANCE TO CHECK WHETHER THE USE OF MICROCHIPS PRODUCED BY COMPANIES OTHER THAN AGILENT!!!) Apart from supplying the slide containing the array, the service includes all the stages described previously (Type 1a), i.e.: (i) qualitative and quantitative RNA analysis using Bioanalyzer (ii) RNA sample marking using fluorescent probe (iii) hybridisation of labelled sample on chip (iv chip scan and data acquisition (v) sending raw data by computer (downloading via web or DVD) (vi) description of the procedure for scientific publishing purposes The service does not include: (i) bioinformatic data analysis (ii) submission of data to public databases Users are requested the slide containing the array supplied with a suitable file for recognising the samples on the grid (e.g. GAL file) and 2 μg RNA at a concentration of 200 ng/μl (Purification using Trizol Invitrogen produces RNA of a suitable quality for performing investigations) |
323.10 |
Other services:
| Code no. | PARTIAL ANALYSIS | Cost per sample (€) |
| B1011 | RNA qualitative and quantitative analysis using Bioanalyzer (multiples of 12 samples) | 32.30 (per 1-12 samples) |
| B1021 | chip scan and data acquisition (user supplies the hybridised slide to be scanned) | 21.10 |
| B1031 | Data storage (images and quantifications) for 1 year in dedicated hard drive. N.B.: data are stored on the Service’s computer for 1 month. After this time, the data will be deleted to recover space on the hard disk. |
5.40 |
2. Agilent microarray bioinformatics analysis
In addition to the service above, it is possible to obtain support for data analysis.
| Code no. | DESCRIPTION | Cost (€) |
| Preliminary consultation for setting up the experimental design during which time an estimate of the overall cost of the analyses requested can be made | No charge | |
| B2001 | Setting-up of experiment: entering data for analysis using GeneSpring software (transcriptome software) | 5.40/sample |
| B2002 | Data analysis to identify genes differentially expressed between two classes (for example: treated vs. non-treated samples, or cancer vs. normal samples). The service includes:
|
161.60 |
| B2003 | Custom analyses by arrangement. This type of service requires active contribution from the user on hypotheses about the experiment in order to define the type of analysis to be performed. For example:
|
86.10/hour |
3. Bioinformatics analysis
| Code no. | BIOINFORMATICS ANALYSIS | Cost (€) |
| B3001 | Basic microarray experiment analysis: an experiment is understood to mean all the data relating to a biological sample. DAMA will perform the complete analysis of a 2-class experiment (for example, diseased and healthy samples), including quality control. Users will receive the results of the processing, including a list of the genes and significant values. N.B.: The analysis will only be performed once the data relating to all the samples in the experiment have been provided. | 340.50 |
| B3002 | Extended basic analysis to include additional sample data and extend the experiment to 2 classes, as referred to at BIO3001. | 170.30 |
| B3003 | Multivariate analysis: the DAMA analyst will provide a thorough analysis of an experiment involving 2 or more classes (for example, clustering, multidimensional scaling, gene ontology, predictability, chromosome mapping, meta-analysis comparing different experiments, long-term scanning, etc). | 79.50/hour |
| B3004 | MIAME data bank: Submission of experiments to the Database (ArrayExpress or GEO). | 33.30 |
| B3005 | Publication support Graphic processing of results, submission to public databases (EBI and NCBI), online publication of supplementary data, etc). | 90.80/ora |
Some of the services/products offered may be provided with the help of other services of the LTTA Laboratory.
Each service includes a description of the procedure and supply of images of any scientific publication purposes.
Prices are shown without VAT and are subject to change according to the cost of consumables necessary for the service (every 12 months).
LTTA c/o CUBO
Via Fossato di Mortara, 70
44121 Ferrara
Main Entrance • Piazzale Eliporto
Web design and
site maintenance
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