Genomnia is a start-up SME founded in October 2008 with the aim of offering deep sequencing and bioinformatic services and collaborations with private and public institutions, covering genomics, transcriptomics and epigenetics projects.
We have relevant experience in molecular biology and bioinformatic analysis of deep sequencing data applied to biomedical projects: transcriptome qualitative and quantitative analysis, miRNA identification and profiling, ncRNA identification and annotation, mutation detection, targeted genome resequencing and analysis.
Our experienced personnel takes care of the planning, optimization and analysis of your sequencing projects. We have upgraded our platform to the Applied Biosystems SOLID™ 5500XL-s with EZBead™ enrichment system, generating up to 180Gb per run . Fragment sequencing range from 25 up to 75bp, PE sequenging up to 75x35bp and mate paired sequencing up to 60x60bp.
Two base encoding system combined with the use of ECC (Exact Call Chemistry) Module allow a level of accuracy of 99.99% which makes it particularly suitable for genomic studies such as variation detection, especially for low frequency variants. The efficient barcoding system up to 96, permits safe and cost-effective multiplexing of large sample size projects. The wide dynamic range and sensitivity make it particularly suitable for measuring accurate fold changes at the low expression levels of RNA.
The 300sq Genomnia laboratories are organized following the ABI guidelines for a SOLiD™ ™ deep sequencing facility:
Library preparations laboratory
- Agilent Bioanalyzer for evaluation of sample acid nucleic integrity and quantification even at picomolar scale
- Syngene G:Box electronic imagines system for any kind of gel
- Nanodrop™ spectrophoto- and Invitrogen Qubit™ fluoro-meter for miniscale quantification of biological materials, including nucleic acids
- Hydroshear® apparatus for nucleic acid fragmentation
- Agarose and acrylamide gel apparatus, including Ambion FlashPage™ system for smallRNA purification.
- ABI 9700 PCR Systems
- Eppendorf Microfuge
- Thermo Scientific Refrigerated centrifuge Multifuge® 3 Plus
- Eppendorf Refrigerated centrifuge 5417R
- Eppendorf Thermomixer
- Covaris™ sonicator
-EZBead™ Enrichment system
- ABI 9700 PCR system
Deep sequencing laboratory
- ABI SOLiD™ 5500 XL-s Sequencer
- ABI 7900HT Fast Real-Time PCR apparatus
- 64-bit Windows XP professional workstation with 8 cores, 16 Gb of RAM and ca. 800 Gb of disk;
- shared memory Linux 64 bit server with 16 processors (dual-Xeon quadcores), 74 Gb of Ram and around 4 Terabytes of disk space;
- six-nodes Linux 64 bit distributed memory cluster with a total of 48 processors (dual-Xeon quadcores), 32 Gb Ram for each node, 1 terabyte of local storage for each node and more than 35 Terabytes of globally shared disk space
- computational cluster, with 32 cores and 14 Terabytes of disk space, dedicated only to SOLiD sequence data production
- shared access to an external HPC facility, for the most compute intensive tasks
Genomnia has invested significant resources in establishing an internal bioinformatic analysis infrastructure, in terms both of the relevant hardware – software infrastructure and of dedicated senior personnel (one senior and one junior analysts) with specific experience in deep sequencing data analysis, system management and quantitative analysis. The aim of the Bioinformatics Analysis Unit at Genomnia is in a first instance the delivery to the scientific partners of high quality SOLiD™ sequence data, unambiguously mapped to the reference genome, annotated and classified with the maximum level of precision and information content and counted with precision. Current bioinformatic analysis skills are strongly focused on sequence identification and annotation. This includes transcriptome analysis, both coding and non coding, of human and model organisms. Quantitative analysis skills (exploratory data analysis; univariate and multivariate approaches; linear model building) and genome-based approaches (mutation analysis; promoter recognition; correlation with gene structure; signal recognition) are also available in house and in partnership with external companies (see Bionformatic Services Brochure).