After section, Hydra regenerate each missing part within 2 to 3 days. This study was designed to allow tracking of gene expression levels during apical and basal regeneration and to compare these different regenerative contexts systematically. We determine that transient early genetic events are generic, i.e. that modulations in gene expression have analogous directions, magnitudes and durations whatever the level along the central body column and orientation of the amputation plane. In turn, early modulated transcripts with sustained expression patterns during regeneration are generally distinct during apical and basal regeneration. Genes that were previously shown to be instrumental in defining the apical organizer (Wnt signalling pathway) are among the first genes to be expressed in the condition where Hydra regenerates its apical part, Wnt3 is actually the only detected transcript encoding a signalling protein already upregulated by 2h. Regarding basal regeneration, we identify a number of transcripts with sustained expression patterns already established by 4h, some of them encoding evolutionary conserved signalling proteins, which are almost exclusively consisting of agonists and antagonists of the BMP signalling pathway. The processed data deposited here are also accessible in a graphical manner from a blast-based web interface available at https://hydratlas.unige.ch Overall design: Samples were taken from regenerating tips of Hydra regenerating apical regions from the 50% (mid-gastric position) or the 80% level (i.e. after decapitation), as well as basal-regenerating tips from the 50% position. Data were sampled at 0, 0.5, 1, 2, 4, 8, 16, 24,36,48 hours post section. In addition, intact animals, apical regions (head), and basal regions (basal disk and lower part of the peduncle) were sampled in homeostatic condition. All samples were produced in biological triplicates from tissue originating from 20 to 25 animals. >> Grant Information << Awarded to Dr. Brigitte Galliot: - Swiss National Science Foundation (SNF grant 31003A-130337, 31003A_149630 & 31003_169930) - NCCR Frontiers in Genetics, Stem Cells & Regeneration project - The Canton of Geneva - The Claraz donation - Human Frontier Science Program (HFSP RHP0016-2010)