Genomic and transcriptomic platform

The genomic and transcriptomic platform was set up in 2017 to coordinate NGS CPTP analyses coming from RNAseq, ChIPseq and ATACseq experiments. Through its expertise and advanced technological facilities the platform respond to the growing bioinformatic and biostatistic needs of the CPTP research teams.

Members
Leader : Manuel LEBEURRIER (IE Inserm)

Activity

Genomic and transcriptomic platform services are designed for biologists and bioinformaticians. The analyses concern mostly RNAseq, ChIPseq and ATACseq experiments. Specific pipelines were developed and deployed on the Genotoul. The platform also carries out analyses regarding variant calling (SNP / INDEL / CNV), gene fusion detections, linkage and association analyses.

Trainings

The platform aims to diffuse its expertise through regular trainings on bioinformatics, biostatistics and computing fields. These are the trainings that have already been performed :

NGS

  • NGS: Yesterday to tomorow sequencing generation story
  • RNAseq analysis: theory and concepts behind differentially expressed genes
  • Galaxy initiation: differentially expressed gene analysis
  • Introduction to command lines and Linux OS
  • Discovery of public databases

 

R

  • R initiation
  • Test theory with R
  • DESEQ2 package: differentially expressed gene analysis
  • Mixomics package: focus on PCA and PLSDA
  • ggPubR package: publication ready figures
  • FlowAI package : automatic or interactive quality control on FCS data
  • FlowClean package : automated identification and removal of fluorescence anomalies in flow cytometry
  • Clustering and classification: from k-means to t-SNE

Operating

In order to respond to the teams needs two operating methods have been adopted:

Project conducting

  1. The client fills a project sheet to describe briefly the context, the scientific issue and the planned study design.
  2. The platform suggests the experimental design and methodologies according to the biological question. Technical details are filled into a technical sheet after agreement between the client and the bioinformatician.
  3. The platform team provides an analysis sheet describing all the steps needed to transform raw data into deliverables. Starting date, time needed and deliverables are specified to the client. The quote is send to the client for signature.
  4. A quote is provided by the platform team. Once the signed quote is received the project will be added to the analysis schedule.
  5. The “wet” part of the project is done by the platform staff in coordination with  members of the client researcher team. A library sheet for quality control is filled in and sent to the client and the bioinformatician.
  6. After sequencing, the bioinformatic analysis is performed and the deliverables are transferred to the client. A result delivery confirmation is signed by the client and sent back to the platform.

 

Project monitoring

With training performed by the genomic plateform, a member of the demanding team will be trained to the common bioinformatic analyses. This person will then be in charge of the future analyses. This responsibility includes the necessity to sending the sheets (project, technical and library) and the quality control to the platform. In this way, the platform will follow the project evolution in order to validate the results obtained in the different key steps of the analysis.

 

Developments

Platform developments are stored in the GitHub repository : CPTPGenomicTranscriptomic.

  • Gene-Attributes : A shiny app that obtains Ensembl gene ID, gene names, the coordinates and description of an input file using biomaRt package.
  • Gene-Attributes-Multiple : A shiny app that obtains Ensembl gene ID, gene names, the coordinates and description of multiple input files using biomaRt package.
  • FlowAIAll : Clean cytometry data using FlowAI R package through a new Rshiny interface
  • ShinyFlowClean : Clean cytometry data using FlowClean R package through a Rshiny interface.
  • shinyheatmap : Web application for enormous biological heatmaps

Equipment

Instruments

  • Bionanalyseur Agilent 2100
  • Sonicateur Covaris M220
  • Sonicateur Diagenode Bioruptor Pico
  • Appareil PCR en temps réel Roche LightCycler 480
Softwares

 

  • IPA (Quiagen)

 

Réservation

Autres informations


Steering comittee
  • Anne Dejean (CR INSERM)
  • Véronique Adoue (CR CNRS)
  • José Enrique Méjia (CR INSERM)
  • Nicolas Blanchard (CR1 Inserm)
  • Olivier Joffre (MCU UPS)
Publications

2018

Célia Dupain Anne C. Harttrampf, Yannick Boursin Manuel Lebeurrier Windy Rondof Guillaume Robert-Siegwald Pierre Khoueiry Birgit Geoerger ; Massaad-Massade, Liliane

Discovery of new fusion transcripts in a cohort of pediatric solid cancers at relapse and relevance for personalized medicine Journal Article Forthcoming

Molecular Therapy, Forthcoming.

Abstract | Links | BibTeX

CNRS

CNRS

Inserm

Inserm

UT3

UT3

TRI-Genotoul

TRI-Genotoul