The main goal of the study is to produce a reference transcriptome for the cnidarian polyp Hydra vulgaris, which will be used for later quantification studies. Both Illumina and 454 reads were mixed in a way to minimize the occurence of frameshifts due to 454 sequencing. Illumina libraries have been prepared from varied regenerating conditions so that an assessment of the modulations in transcripts levels during early hydra regeneration is possible.