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Sequencing Platform of Nice

This functional genomics platform was created in 1999 by Dr. Pascal Barbry of the IPMC (Institute of Molecular and Cellular Pharmacology). Initially orientated towards design, production and analysis of DNA chips, the platform has contributed to opening up this technology to a wider academic community. Today the platform continues to provide services for analysis of commercial DNA chips (Agilent, Affymetrix), whilst developing a large part of its activity around high-throughput sequencing services (SOLiD™ 5500XL), such as smallRNA-Seq, RNA-Seq and CHiP-Seq.

Equipment :
Pre-sequencing : Nanodrop™, Bioanalyzer, Qubit®, CovarisS2, Ion Chef, NeoPrep
Single Cell Analysis : Fluidigm C1, Fluidigm Biomark
Sequencer : Illumina NextSeq500,Ion Torrent PROTON, Ion Torrent PGM
DNA chips : High-Resolution Microarray Agilent Scanner, Affymetrix station

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Quality Assurance/ Certification :
All platform activities are ISO9001 certified since 2006. From the outset, the development of the Médiante information system (http://www.genomique.info:8080/merge/index) has provided all platform collaborators with an online tracking system, allowing them to track the status of their samples and obtain simplified access to all their results.

Bioinformatics analysis :
The Nice platform offers the following services :
Raw sequence data (.csfasta) + quality scores (_QV.qual) upon request + sequence and control quality reports (FastQC) including :
- checks for contamination (barcodes, adapters, rRNA…).
- data filtering and cleaning, and generation of various summary tables.
- alignment of reads against a reference sequence (STAR, bowtie2, lifescope).
-  storage in .BAM alignment files, . BW files with coverage of all secondary analysis files on the information portal of the Mediante platform.
http://www.genomique.info:8080/merge/index) which displays the information via the custom tracking system of the UCSC genome browser.

DNA analysis :
- Search/annotation of SNPs and INDELs (gene involved, change of amino acid, consequence (nonsense, coding…), Swissprot identification, gene description, dbSNP hg19 link to rs, 1000genomes / MAF, functional predictions in dbSNPFv2.0 for non-synonymous coding, complete genomics, link to the NCBI gene, link to OMIM, position type (exon/ intron position, HGVS nomenclature, genomic/transcrip/prot) (ionTorrent server)
- ChIP-Seq : Search for binding sites (transcription factors), histone marks, pol-II (MACS2, HOMER, Meme),
- De novo assembly (genomes < 50 MB ; Abyss, Spades, Velvet, SOAP)
RNA analysis :
- de novo RNA-Seq assembly in a colour space via an in-house de novo RNA-seq (velvet+ oases+asid) assembly pipeline,
- RNA-Seq transcript assembly. Identification of alternative splice sites (lifescope v2.5.1).
- RNA-Seq differential analysis (standardisation and comparison of different conditions) (DESeq2, package R bioconductor), + annotation of results. Provision of a feedback report in PDF format, including a general quality control summary of the experiment + differential expression analysis.
-  smallRNA-Seq : Identification of the species detected (miRNAs, piRNAs, snoRNAs, tRFs, ensembl ncRNAs, fRNAdb) via an in-house pipeline following smallRNA mapping with lifescope v2.5.1,
- smallRNA-Seq : search for expression zones of non-annotated small RNAs (MACS),
- smallRNA-Seq : differential expression analysis (standardisation and comparison of different conditions) (DESeq2, package R bioconductor), + annotation of results. Provision of a feedback report in PDF format, including a general quality control summary of the experiment + differential expression analysis.

For further information : http://www.genomique.info

Conatcts :
Platform Manager : Pascal Barbry (barbry@ipmc.cnrs.fr)
Production manager : Virgninie Magnone (magnone@ipmc.cnrs.fr)
Bioinformatics manager : Kevin Lebrigand (lebrigand@ipmc.cnrs.fr)

Institut de Pharmacologie Moléculaire et Cellulaire du CNRS,
UMR7275, CNRS/Université de Nice-Sophia-Antipolis,
660, route des lucioles, 06560 Valbonne-Sophia-Antipolis.


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