WP1 - Sample collection and assays-by-sequence

WP Leader: Dr. Celine Sabatel – DIAGEN​
Deputy WP leader: Dr. Hervé Acloque – INRA

Involved partners: DIAGEN, INRA, UEDIN

Background
Functional annotation of pig and chicken genomes aims at identifying functional elements (coding and regulatory) that are active, poised or repressed in organs and tissues. As the activation status of these functional genome sequences varies not only between cells and tissues but also over time, it is necessary to take into account the dynamics (“switches”) of the functional genome from embryo/fetus to adult life. To achieve these annotations, molecular assays known to provide core information on gene transcription and regulatory elements’ activity are carried out on collections of tissues representing different developmental and adult stages. No datasets or samples representing fetal or embryonic stages are available in the FAANG data portal for these two species and GENE-SWitCH will fill in this gap.

Objectives

• To establish a collection of cryopreserved tissues in pig and chicken at three developmental stages on four biological replicates (two males and two females).
• To perform core molecular assays required for the functional annotation of the pig and chicken genomes on seven different tissues for the three developmental stages.

Tasks​​

• T1.1 - Sampling pig tissues
• T1.2 - Sampling chicken tissues
• T1.3 - Molecular assays: Chip-seq and ATAC-seq
• T1.4 - Molecular assays: RNA-seq
• T1.5 - Molecular assays: WGBS-RRBS
• T1.6 - Molecular Assays: Hi-C Capture

WP1 - Sample collection and assays-by-sequence

WP2 - New annotation maps of pig and chicken genomes

WP3 - FAANG Data Coordination, Standardisation and Integration

​WP4 - Improving predictive models for genomic selection

​WP5 - Influence of maternal diet on epigenetic programming of offspring

​WP6 - Outreach, dissemination and training

WP7 - Project management and consortium coordination

​WP8 - Ethics