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Sequencing platform

Presentation

Presentation of the IGFL's Sequencing platform

The IGFL’s sequencing platform undertakes deep sequencing projects of different scales with the latest next generation sequencing (NGS) technology.

Since 2012, we've acquired considerable expertise via a range of unique and diverse projects, often requiring the development of customised methodologies.

The platform operates predominantly in a collaborative mode with both academic and private sectors.

 

Activities

The sequencing platform designs and executes - in close concertation with users -  projects with a wide range of applications. Sequencing facilities allow for small to large scale projects, and for long or short reads. We recommend you contact us as upstream as possible to determine the optimal sequencing strategy for your project.

Numerous applications and domains are possible given the different equipment available, including for example: de novo sequencing of small and medium sized genomes, RNA (mRNA, microRNA, Dual RNAseq), ChIPseq, transcriptomic and metagenomic studies (bacterial diversity, eDNA), screening projects (e.g. CRISPR), as well as sequencing of targeted regions (e.g. gene panels) and amplicons.

Partner of the Equipex Spatial-Cell-ID project, the platform is also equipped with a Chromium Controller (10X Genomics) allowing the realization of Single Cell RNA (gene expression) or DNA ( ATAC-seq) analyses.

The platform can propose certain primary bioinformatics analyses to users (mapping on reference genomes of a model species, assembly of small sequenced genomes) but not the secondary analyses nor the statistical analysis of data. We provide advice on different analytical tools available locally (e.g. the Galaxy analysis platform) or via academic or private sector subcontractors (several of which have previously collaborated with the platform).

In parallel with the development, testing and implementation of new sequencing protocols, the PSI platform conducts its own research in the field of environmental DNA (eDNA), studying in particular the diversity of living organisms at different levels (vertebrates, bacteria,...) through various approaches (metagenomics, barcoding, metabarcoding, impact studies,...) within complex natural environments (water, soil,...) or microbiota.

The platform develops and executes new protocols.

 

Equipment

The platform is equipped with 5 high screening capacity sequencers of 2 technology types (Illumina for short-reads and Oxford Nanopore Technologies for long-reads).

Technologies

 Sequencers/Equipment 

Sequence length

Number of reads/run

Duration of sequencing

Applications

Illumina (SBS)

 

Nextseq500

Single End : 75 or 150 pb

Paired End : 2x75 or 2x150 pb

130 - 400 million 12 to 30 hours

Trancriptomics(bulk or single cell)

Targeted DNA sequencing (e.g. exomes)

Whole genome sequencing (de novo or re-sequencing)

Methylation and ChIP seq

Screen CRISPR

MiSeq

Single End : 50 to 300 bp

Paired End : 2x25 to 2x300 bp

1, 4, 15 or 25 million 17 to 56 hours

Screening Amplicon sequencing (e.g. metagenomics, Ampliseq or Panel)

Small genomes (re)-sequencing

 

Oxford Nanopore Technologies

 

Minion

Several kb
 
Thousand to million Up to 72 hours DNA, RNA, amplicons sequencing with
long fragment applications

 

2 Mk1C

 

 

10X Genomics

 

Chromium Controller

Single Cells or Nuclei encapsulation  Up to 10k cells -

Transcriptomics Single Cell (3’ mRNA, 5’ mRNA)

Single Cell ATAC seq

Users can also benefit from the platform's equipment to construct DNA and RNA sequencing librairies (Qubit 4.0 Invitrogen, Tapestation 4150 Agilent, Nanodrop 2000 Thermofisher, S220 Focused-ultrasonicator Covaris, ….).

The platform's confined laboratory facilities are adapted to working with nucleic acids available either in limited quantity and / or degraded quality. Procedures and infrastructure are in place to prevent the rish of contamination by nucleic acids of exogenous origin.

 

SuPport and ADVICE

We can assist you at the different stages of your project including experimental design, the sequencing phase, and can also provide training regarding the qualification of your samples and construction of libraries for sequencing.

 

Organisation

The platform interacts with users on a regular basis and during internal seminars to make a review of projects realized and identify future avenues for development and functioning.

 

Training

The platform provides several training opportunities (in French):

 

Costs

Please contact us (Sandrine HUGHES or Benjamin GILLET) for further information.