title: RNA-Seq and metatranscriptomics Danio rerio
design: Total RNA from intestine and kidney samples obtained from the fish exposed to DMSO or antibiotics was extracted using the Maxwell RSC simplyRNA Tissue kit (Promega) with an automated Maxwell RSC 48 Instrument in accordance with the manufacturer's instructions. For the samples obtained from the sublethal infection, the quantity of RNA was measured in a Qubit 4 Fluorometer (Invitrogen) using the Qubit RNA HS Assay Kit (Invitrogen); after this, RNA integrity was analysed in an Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA) according to the manufacturer's instructions. All the samples that passed the quality control tests were used for Illumina library preparation. Double-stranded cDNA libraries were constructed using the 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).