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Submit your data to MicroScope
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of MicroScope's functionalities
Get information about Delivery of Service offer provided by LABGeM in the context of the MicroScope platform, and initiate a new Delivery of Service for data submission & integration.
Delivery of Service Offer
Service features
Access to the MicroScope web site (hosted at Genoscope), which provides an environment for expert annotation and comparative genomics.
Technical support is provided by LABGeM for all users.
Bioanalysis / Scientific expertise by LABGeM is restricted to « Collaborations » only (
contact us
for further information).
Data conservation and backups (during the whole duration of the service).
Computation updates (following the internal rules of the laboratory).
Data / sequence updates.
Type of projects
Genome / Metagenome
RNAseq
Description
Genome project: Annotation and comparative analyses of finished or draft genome sequences. For public genomes from GenBank, we only integrate original annotations of complete genomes.
Metagenome project: Annotation and comparative analyses of assembled metagenomic sequences. Currently, we are able to integrate datasets below 20 Mb of contigs per bin.
Delivrable
Syntactic and functional annotation.
Metabolic network reconstruction.
Data integration in our database (PkGDB).
Service features
Comparative genome analysis and synteny computations with all genomes stored in PkGDB and with NCBI RefSeq genomes.
Metabolic network exploration using KEGG and BioCyc resources.
Users can request data suitable for submission to EMBL sequence database.
Description
RNAseq project: Map a RNAseq dataset to a reference genome and perform differential expression analyses.
Requirements
Sets of NextGen Sequencers
untrimmed
reads (fastQ format) corresponding to experimental conditions.
A reference genome (if not already loaded into the platform please see Genome / Metagenome service offer).
Delivrable
Succinct reads quality reports.
Complete mapping Statistics reports.
Access to raw read count analyses for each experimental condition.
Test for gene differential expression between pairs of experimental conditions.
Service features
Quality control of NextGen Sequencers reads.
Reads mapping on reference genomic sequence(s).
Read coverage visualization using
Integrative Genomics Viewer (IGV)
Export all results in spreadsheet compliant format for subsequent analyses.
Description
Evolution project: SNP/indels detection among different evolved strains by comparison with a reference genome.
Requirements
Sets of NextGen Sequencers
untrimmed
reads (fastQ format) corresponding to experimental conditions.
A reference genome (if not already loaded into the platform please see Genome / Metagenome service offer).
Delivrable
Succinct reads quality reports.
Complete mapping Statistics reports.
Access to complete inventory of polymorphic sites.
Preliminary analyses (inventory of synonymous/non synonymous mutations, transitions/transversions,...).
Service features
Quality control of NextGen Sequencers reads.
Reads mapping on reference genomic sequence(s).
Polymorphic sites detection and scoring.
Export all results in spreadsheet compliant format for subsequent analyses.
Access
Fee / Prices:
Free for academics.
Sales quote available on demand for non-academics (
contact us
for further information).
Personal login and password for each user, and access rights defined at the level of user groups.
Scientific publications
Proper acknowledgement and citation of the MicroScope publication are required in all scientific publications linked to the project.
Please use the following sentence for acknowledgements: "The LABGeM (CEA/Genoscope & CNRS UMR8030), the France Génomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d'Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09, ANR-11-INBS-0013 and ANR-21-ESRE-0048) are acknowledged for support within the MicroScope annotation platform."
MicroScope publication:
Vallenet D, Calteau A, Dubois M, Amours P, Bazin A, Beuvin M, Burlot L, Bussell X, Fouteau S, Gautreau G, Lajus A, Langlois J, Planel R, Roche D, Rollin J, Rouy Z, Sabatet V, Médigue C
«MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis»
Nucleic Acids Res. 2019 Oct. 24
Data Submission
Data submission performed by the user, according to the specifications concerning each project type (genome/metagenome, RNAseq, evolution).
Set up a new project?
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