Genomics and bioinformatics

The two main Genomics platforms are located in Nice (IRCAN, Gael Cristofari) and Sophia-Antipolis (IPMC, Pascal Barbry), are complementary and have recently merged into the same structure, UCA GenomiX (certified IBiSA in 2017). They are open to local, especially SIGNALIFE members as well as external academic or non-academic members of the scientific community. Biostatistical and bioinformatics analyses are included in their offer. There is also a genotyping platform, equipped with a Sequenom in Nice (CAL, Gerard Milano). Additional Molecular Biology platforms have been developed at C3M and iBV, and notably include a Genome Editing facility (iBV) with the latest CRISPR / Cas9 technology for targeted genome modifications in various model organisms. All institutes are fully equipped with “traditional” sequencing and several types of qPCR machines.

The platform has been created in 1999, ISO9001 certified since 2006, and is a partner of the “France-Génomique” infrastructure in biology and health (coordinator: P. Barby, IPMC; https://www.france-genomique.org). The lab is equipped with next-generation sequencing (NGS) Illumina NextSeq500, Ion Torrent PROTON and an Agilent array scanner and provides a wide range of expertise to academics and clinicians. Optimal protocols are proposed, notably for directional RNA and small RNA sequencing (miRNAs, piRNAs …), total RNA depleted of ribosomal RNA, mRNA (polyA+ purifications), CHIP-SEQ and DNA resequencing. Recent developments have been focused on single-cell RNA-seq analyses (Fluidigm C1, Chromium Single Cell 10X Genomics) and long reads sequencing technologies (MinION, Oxford Nanopore Technology).

    

The platform is dedicated to genetic variation and gene expression analyses. It provides knowledge and access to cutting-edge, medium-to-high throughput tools and technologies. Equipment available includes systems dedicated to NGS (Illumina NextSeq500, Ion Torrent PGM, OneTouch), chromatin-IP (ChIP) (Bioruptor pico, IP-Star compact, Pippin prep) as well as bioassays and imaging systems. Ongoing development are focusing on long reads sequencing (Oxford Nanopore Technology).

This platform provides intramural expertise and technology to process large data sets using an in house Galaxy server. We aim at developing this platform further to provide extended expertise and tools by recruiting one engineer and 1 team with a focus on Bioinformatics.

Equipment: Galaxy Web Server (Dell PowerEdge R920 with 4 processors 12 cores, 512 Go RAM, 1.8 To in 2 internal drives – external drives for storage).

Contact : lmartin@unice.fr

This platform provides expertise in a number of techniques, including targeted genome editing (CRISPR/Cas9) in the different models hosted by iBV, strategy and vector design, tailor-made protein purification.

Equipment: 1 FPLC (Bio-Rad – NGC), 1 FPLC (Pharmacia – AKTA pure), Imager (Vilber Lourmat – Fusion FX7), Imager (Odyssey – LiCor), microvolume spectrophotometer (DeNovix – DS11), vacuum concentrator (Eppendorf), lyophilisator (Hetosicc-flexiDry).

Contacts : Virginie Virolle: vvirolle@unice.fr (04 92 07 68 71)