Infected head kidney
RNA was isolated from the head kidney and intestine samples obtained from gilthead sea bream control and infected with the bacteria Photobacterium damselae subsp. piscicida (n=4). For this we used the Maxwell RSC simplyRNA Tissue Kit (Promega) with an automated Maxwell RSC 48 Instrument following the guidelines outlined by the manufacturer. The quantity of RNA was measured with a NanoDrop ND-1000 (NanoDrop Technologies, Inc.); afterwards, RNA integrity was analysed in an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA, USA) according to the manufacturer's instructions. All samples passed the quality control tests (RIN  8).. Double-stranded cDNA libraries were constructed using TruSeq Stranded mRNA LT Sample (Illumina, San Diego, CA, USA). Paired-end 150 bp (PE150) sequencing was performed on an Illumina NovaSeq 6000 sequencer. Both library preparation and sequencing were performed at Macrogen, Inc. (Seoul, Republic of Korea).