The sequencing platform of Lille Go@l
GO@L GEnOmique @ Lille) is the genomics platform of the PLBS unit (UAR2014-US41). It provides a wide range of solutions and expertise in the field of high-throughput genomics. The technical approaches used are mainly based on high-throughput sequencing and DNA chips. The platform is the result of the merger of two specific and long-established entities, TAG (Transcriptomic and applied genomic) and GFS (Functional and structural genomics), and over the years has developed recognised expertise in microbiology and human genomics.
GO@L offers RNA quantification approaches (mRNA, small RNA, lncRNA, isoforms, single-cell, spatial) in a targeted manner or at the genome level for differential expression analyses, approaches for the identification and quantification of DNA anomalies (target-Seq, WES, WGS), approaches for DNA-DNA and DNA-RNA interactions and for the regulation of gene expression (ChIP-Seq, RIP-Seq, DNAse-Seq, methylation) GO@L has also developed a specialisation in microbial genomics with whole genome sequencing applications for bacteria and viruses, classical and dedicated RNA-seq applications such as differential RNA-seq and 5’RACE-NGS and a complete pipeline of targeted metagenomic studies.
The GO@L team is composed of half molecular biologists specialised in high throughput and half bioanalysts and bioinformaticians who are experts in the analysis of the data generated and the development of dedicated solutions.
Equipment
- Nova-Seq 6000 Illumina,
- MiSeq Illumina,
- Chromium 10X Genomics,
- Tapestri
- DNA Array genotyping Agilent,
- NanoString,
- MinION Oxford Nanopore Technologies.
Expertise
- Sequencing and re-sequencing of whole genomes (human, bacteria, parasites, viruses),
- Resequencing of human exomes of various qualities (FFPE, PBMC),
- Targeted sequencing (amplicons, captures),
- RNA-Seq, 3'RNA-Seq and sRNA-Seq (human, mouse, bacteria),
- 5'-RACE-NGS (full-length RNA-Seq),
- Identification of transcription sites (TSS) by RNA-Seq,
- scRNA-Seq (10X genomics, tapestri),
- spatial transcriptomics (10X visium),
- 16S targeted metagenomics,
- DGE Microarray (Agilent Technologies),
- DGE without amplification (NanoString technology),
- qRT-PCR
Bioinformatics
Bioinformatics analysis: GO@L has developed, for collaborative projects, analysis expertise associated with the applications proposed by the platform. For genomic characterisation: alignment on reference, assembly, detection and annotation of variants, Mendelian transmission study, clonality study. For transcriptomics: DGE, RNA splicing analysis, gene prediction/discovery, RNA-IP. For targeted metagenomics: taxonomic assignment, diversity assessment, dysbiosis measurement.
- WACA, cghRA: Normalisation and quantitative analysis of copy number anomalies (doi: 10.1093/nar/gkp1215, doi: 10.1093/bioinformatics/btx309)
- MICRA: Automatic whole genome sequencing analysis pipeline, characterisation of bacterial genomes (doi: 10.1186/s13059-017-1367-z)
- DiNAMO: Identification of sequencing errors (doi: 10.1186/s12859-018-2215-1)
- V-ASAP : Viral genome amplicon-seq assembly tools without reference (doi: 10.1016/j.jcv.2019.104206, doi: 10.1016/j.virol.2019.03.006)
Main Achievements
Most of GO@L’s activity is carried out in collaboration with a research laboratory. GO@L has thus been a partner in many large-scale projects financed by major funding agencies (ANR, ERC, H2020, etc.). The research laboratory usually leads the project and the GO@L platform supports the project by providing its expertise and know-how. However, from time to time, our platform acts as a project leader and carries out work itself, usually on the development and application of methods or protocols ((Siegwald et al., 2017; Hot et al., 2011; Amman et al, 2018) ) or on the development or improvement of bioinformatics solutions (WACA (Leprêtre et al., 2010), MPAgenomics (Grimonprez et al. 2014), vidjil (Giraud et al., 2014), MICRA (Caboche et al, 2017), cghRA (Mareschal et al. 2017), DiNAMO (Saad et al., 2018), V-ASAP (Maurier et al, 2019)). Several opinion reviews on the reality of the field and on the perspectives of the field have also been published by the platform (Jardin et al., 2013; Caboche et al., 2014(a); Caboche et al., 2014(b); Audedert et al., 2014; Audebert et al., 2018).
Last update February 2022
Certification / Quality Assurance
Labels
IBISA
Platform Managment
Martin Figeac
David Hot
PLBS UAR 2014-US
Pôle Recherche
1 place de Verdun
59045 Lille cedex