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  • Project Manager
  • Research Engineer
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About

The platform is mainly using Illumina Next Generation Sequencing for transcriptomics and epigenomics (mainly using RNAseq and ChiPseq approaches).  It is accessible to Research Units from the Campus, the network and to external teams. The plaform has wet lab (sample quality control and processing) and dry lab (bioinformatics and statistics) activities.

It has two functioning modes: service (sequencing of libraries prepared by the users and providing of the raw data) and, most often, collaboration (in this case, the platform is involved in all the steps of the project, from the experimental design to the statistical analysis of the data).

Submission of a project to the platform is a TWO STEP process:

FIRST STEP:  fill the general project submission form for the Biomics pole

SECOND STEP: fill the appropriate form for the platform according to wether your project is a collaboration or a service

citech-puce    For collaborative projects, a Application Form has to be downloaded pf2_formulaire-soumission-collaboration and sent to Jean-Yves Coppée.

citech-puce   For service projects, a Application Form has to be downloaded pf2_formulaire-soumission-service and sent to Jean-Yves Coppée. In case of multiplexing, choosing the right indexes  is of  paramount importance. Please look at the following  : Index compatibility for sequencing before choosing your indexes.

Since 2008, the platform has been involved in more than 210 projects. These cover a wide range of organisms (viruses, bacteria, fungi, protozoans, mammals) and are centered on the main biological questions under study at the Pasteur Institute.

They are focused on the following themes (not exhaustive):

  • Study of virulence factors
  • Study of host-pathogen interactions, and host response to infection
  • Study of the effect of environmental pressures (stress, immune pressure, drug pressure …) on the pathogen
  • Comparison of inter-species transcriptomes
  • Identification of regulatory targets (virulence, motility...)
  • Developmental Biology

Events

Training on the Agilent Bioanalyzer

Building: Biotop, 2ème etage – Room: 2A – Address: 28 Rue du Docteur Roux, Paris, France
2017-09-08 00:00:00 2030-09-07 23:59:00 Europe/Paris Training on the Agilent Bioanalyzer A SPOC for using the Agilent Bioanalyzer Training sessions for the use of the Bioanalyzer, organized at the Transcriptome and Epigenome platform of the Biomics pole, are now replaced by a SPOC, available 24 […] 28 Rue du Docteur Roux, Paris, France

Projects

Tools

Services

Pushing the Limit: A Complete Solution for Generating Stranded RNA-Seq Libraries from Picogram Inputs of Total Mammalian RNA

With challenging samples, like RNA isolated using laser capture microscopy, it is difficult to obtain 10 ng of starting material; additionally, rRNA depletion leads to sample loss, undermining robust library preparation. The new release surpasses […]

Index compatibility for sequencing

Illumina uses a green laser to sequence G/T and a red laser to sequence A/C. At each cycle at least one of two nucleotides for each color channel need to be read to ensure […]

Protocol for library construction available allowing to perform RNAseq from low input

The SMARTer Ultra Low Input RNA Kit for Sequencing – v3 incorporates Clontech’s patented SMART (Switching Mechanism at 5’ End of RNA Template) technology. This technology uses the template switching activity of reverse transcriptase […]

Single Cell

RNAseq is routinely used for the characterization of bulk transcriptome. Nevertheless, Interest in single-cell whole-transcriptome analysis is growing rapidly, especially for profiling rare or heterogeneous populations of cells. In collaboration with the Centre d’Immunologie […]

CHIPSeq

ChIPSeq is used for the analysis of the interactions between the genome and nucleic acids binding proteins like transcription factors or chromatin associated proteins. Starting from the IPs / inputs, the PF can perform […]

RNAseq

RNAseq is used for gene expression profiling of different populations of coding or non coding RNAs as well as for the annotation of the genome (exhaustive mapping of TSS, identification of splicing isoforms…). Several […]

Equipments

Sequencing Systems • Illumina • MiSeQ

Here is the list of type runs on MiSeq :List_runs_MiSeq 

BioAnalyzer • Agilent • Bioanalyzer 2100

Our Bioanalyzer 2100 is dedicated to the microfluidic  electrophoresis of nucleic acids (DNA, RNA). Depositing the samples is done on specific chips depending on the type of sample. Electrophoresis is fast and provided quantitative […]

LabChip • Caliper •

freely accessible to the campus

Sequencing Systems • Illumina • Hiseq 2500 (1To)

Illumina sequencing devices which are shared with other platforms of the Biomics Pole

Publications