The Genomic Unit staff have 15 years of experience in Next Generation Sequencing technologies and bring this know-how to support your research projects. We use state of the art technology platforms and provide comprehensive support for many applications including RNA-seq, DNA-seq, ChIP-seq, WGS, WES, gene panels as well as Single Cell profiling (10X Genomics) and Single Molecule sequencing experiments(ONT). We provide support for clinical trials, including the SAGITTARIUS study funded by the European Union's Horizon Europe program.
The unit provides professional support for the different phases of a research project, from the optimisation of the experimental design to the functional interpretation of the results obtained. This includes identification of the ideal methodological approach to achieve the experimental objective, quality control of nucleic acids, generation of indexed fragment libraries, sequencing and analysis of results for selected applications. We are available to customize protocols for specific needs. Sequencing results are delivered via the web, using a platform with an intuitive interface and password-protected access.
Innovation
Our understanding of how the genome works is advancing rapidly, thanks in part to the constant developments of NGS-based analysis methods. Keeping pace with technological advances requires constant commitment. We are constantly implementing new approaches to keep our expertise up to date and make it available to the scientific community. We offer single molecule sequencing (Oxford Nanopore Technologies) and single cell applications on Chromium X instruments (10X Genomics).
Quality
The Genomics Unit boasts over a decade of expertise in genomic technologies, beginning in 2008 with the acquisition of an Illumina Genome Analyzer II sequencer. Over the years, the Unit has expanded its capabilities, incorporating certified diagnostic platforms such as the MiSeqDx and NextSeq550Dx, which are currently operational. Additionally, the Unit benefits from access to a NextSeq2000 and a NovaSeq6000 system based at the Catania site. We perform quality controls throughout the entire workflow and implement GLP (Good Laboratory Practice) standards. Our protocols and operating procedures are regularly updated to ensure the highest levels of efficiency and performance. We actively collaborate as operational partners in Clinical Trials. Cogentech is an ISO 9001:2015 certified company.
Certified laboratory
UNI EN ISO 9001:2015 n. IT324391
Quantity and Quality control (Qubit and TapeStation)
DATA ANALYSIS
Complete service list
NGS data analysis available for selected applications (ChIPSeq and RNASeq, DNASeq, LowPass WGS, ONT applications, inquire for details) including QC, filtering, alignment to reference, identification of DEGs/peaks, annotation, visualization.
Affymetrix® Microarray
Complete service list
Genotyping, CNV or Molecular karyotyping
Gene expression profiling from totalRNA, mRNA, miRNA
FAQ
This is a list of most frequently asked questions regarding facility activities:
Our Genomic Unit offers a broad portfolio of applications for DNA, RNA, epigenetic, single cell and single molecule approachesn and bioinformatic support for selected applications. Please contact us for additional details.
The facility routinely performs checks to verify both the quantity and quality of the starting material, intermediate products, and final libraries (using the TapeStation to assess integrity and the Qubit to quantify DNA/RNA concentrations).
Certainly. They should preferably be provided to the Genomic Unit at a concentration of 2 nM, along with the average library size (expressed in bp) and details of the indices used. We will still perform a concentration check on the submitted libraries and, upon request, also re-verify the library size using the TapeStation.
The facility is equipped with an Illumina NextSeq550Dx, an Illumina MiSeqDx, and a sequencer from Oxford Nanopore Technologies. For experiments requiring higher throughput, we also have access to an Illumina NextSeq2000 and an Illumina NovaSeq6000Dx located at our Catania site.
To minimize sequencing failure, we run a QC after every major step of your project. Unfortunately, sequencing can sometimes fail due to reasons (e.g. instrument malfunction, reagent formulation, technical error, sample issue). If our assessment indicates the failure is caused by our laboratory, we will repeat the analysis at no-extra cost.
We will contact you to discuss available options. If possible, a replacement sample can be submitted, otherwise we can still process the sample, at researcher’ responsibility.
All samples must be shipped at controlled temperature (RNA on dry ice, DNA at +4 °C). Please plan your shipment accordingly to avoid delivery after 5:00 pm on Fridays or on weekends. Shipments will not be collected at these times. It is your responsability to make sure that temperature control is guaranteed. If sample shipment crosses an extra-EU border, custom duties will be applied in the quotation.
Our shipping address is:
Genomic Unit c/o Cogentech
Via Adamello 16
20139 Milano (IT)
Leftover samples will be stored for 6 months after processing, then discarded without prior advice. We can ship back remaining samples before that deadline, with shipping costs at your charge.
Raw data will be available for download in fastq.gz format using a password protected web-based delivery system. In case data analysis is included, additional results will be delivered in txt or jpg format.
Staff and Contacts
Simone Minardi
Simone Minardi graduated in Biological Sciences at the University of Pavia in 1997. After two years at the Mario Negri Institute in Milan, he decided to focus his energy on a new technology, the microarrays. He started developing this post-genomic approach at the European Institute of Oncology, before joining IFOM and later Cogentech to head the Genomic Unit.
Claudia Valli
Claudia Valli graduated in Biological Sciences at the University of Milan in 2005. Then obtained a PhD in Pharmacological Research at the Mario Negri Institute in Milan. Driven by the passion for technological aspects of research, in 2009 she joined the Microarray Unit, now Genomic Unit, where she currently works as a senior technician.
Mirko Riboni
After graduation as a Biomedical Laboratory Technician, Mirko Riboni started to work in a research group at Tigem Milano in 1997, specializing in the use of Sanger method automatic sequencers and moved to IFOM three years later.
Following the natural evolution of his career path, his activity continued in the Genomic Unit of Cogentech where, using next generation sequencing technologies, he helped supporting research projects over the last 15 years.
Francesca Doyle
Francesca Doyle graduated in Molecular Biology and Genetics at University of Pavia in 2022. During her studies she did an internship in a research group at San Raffaele Hospital in Milan where she approached Next Generation Sequencing technologies, NGS. When she completed her studies she continued working with these cutting-edge technologies joining the Genomic Unit of Cogentech as a junior technician.
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