SRX712720 wAR1 SRP048186 PRJNA261810 Eggs were obtained from natural spawning Solea solea adults. Those fish were grown from juveniles obtained from Solea BV (Ijmuiden, Netherlands) and bred at PFOM fish facility (Ifremer, Brest, France). Fertilised eggs were selected by buoyancy and were put in 60 l incubators at 14°C (water temperature) until hatching. One day post-hatching (dph) larvae were distributed among  cylindrical fibreglass 67 l tanks (5300 larvae per tank). Throughout the experiment, water salinity and oxygenation were maintained at 35‰ and more than 6 mg/l, respectively. Water temperature was progressively increased from 14°C to 16°C and then to 20°C between 1 and 5 dph for acclimation purposes. Embryos at stage 7/8 (gastrula 30 h post fertilisation) were exposed to all-trans RA (ATRA, Sigma-Aldrich, Ref R2625) at final concentration of 10 nM during 3h and collected at 33 h post fertilisation. Samples were washed with DEPC water, frozen in liquid nitrogen and stored at −80 °C until analysis. Pools homogenization was carried out in the Fast-prep FG120 instrument (Bio101) using Lysing Matrix D (Q-Bio- Gene) for 40 s at speed setting 6. Total RNA was isolated from 50 mg of tissues or pools of embryos and larvae using the RNeasy Mini Kit (Qiagen). RNA integrity was further investigated using the Bioanalyzer 2100 (Agilent Technologies) before preparation of library. Illumina libraries were constructed at MGX platform (Montpellier, France) using TruSeq RNA Sample Preparation Kit v2 according to manufacturer’s protocols. Briefly, 0.5 μg of total RNA was used for poly-A based mRNA enrichment selection using oligo-dT magnetic beads followed by fragmentation by divalent cations at elevated temperature resulting into fragments of 80-250 nt, with the major peak at 130 nt. First strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second strand cDNA synthesis performed using RNAseH and DNA Pol I. Double stranded cDNA was end repaired, 3´adenylated and the 3´-“T” nucleotide at the Illumina adaptor was used for the adaptor ligation. The ligation product was amplified with 15 cycles of PCR. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode 2 x 100 bp in a fraction of a lane (1/7 ) of a HiSeq2000 sequencing system (Illumina, Inc) following the manufacturer’s protocol. SRS710974 SAMN03076578 wAR1 RNA-Seq TRANSCRIPTOMIC RANDOM 200 0 Application Read Forward 1 1 Application Read Reverse 101 Illumina HiSeq 2000 SRX712721 wAR2 SRP048186 Eggs were obtained from natural spawning Solea solea adults. Those fish were grown from juveniles obtained from Solea BV (Ijmuiden, Netherlands) and bred at PFOM fish facility (Ifremer, Brest, France). Fertilised eggs were selected by buoyancy and were put in 60 l incubators at 14°C (water temperature) until hatching. One day post-hatching (dph) larvae were distributed among  cylindrical fibreglass 67 l tanks (5300 larvae per tank). Throughout the experiment, water salinity and oxygenation were maintained at 35‰ and more than 6 mg/l, respectively. Water temperature was progressively increased from 14°C to 16°C and then to 20°C between 1 and 5 dph for acclimation purposes. Embryos at stage 7/8 (gastrula 30 h post fertilisation) were exposed to all-trans RA (ATRA, Sigma-Aldrich, Ref R2625) at final concentration of 10 nM during 3h and collected at 33 h post fertilisation. Samples were washed with DEPC water, frozen in liquid nitrogen and stored at −80 °C until analysis. Pools homogenization was carried out in the Fast-prep FG120 instrument (Bio101) using Lysing Matrix D (Q-Bio- Gene) for 40 s at speed setting 6. Total RNA was isolated from 50 mg of tissues or pools of embryos and larvae using the RNeasy Mini Kit (Qiagen). RNA integrity was further investigated using the Bioanalyzer 2100 (Agilent Technologies) before preparation of library. Illumina libraries were constructed at MGX platform (Montpellier, France) using TruSeq RNA Sample Preparation Kit v2 according to manufacturer’s protocols. Briefly, 0.5 μg of total RNA was used for poly-A based mRNA enrichment selection using oligo-dT magnetic beads followed by fragmentation by divalent cations at elevated temperature resulting into fragments of 80-250 nt, with the major peak at 130 nt. First strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second strand cDNA synthesis performed using RNAseH and DNA Pol I. Double stranded cDNA was end repaired, 3´adenylated and the 3´-“T” nucleotide at the Illumina adaptor was used for the adaptor ligation. The ligation product was amplified with 15 cycles of PCR. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode 2 x 100 bp in a fraction of a lane (1/7 ) of a HiSeq2000 sequencing system (Illumina, Inc) following the manufacturer’s protocol. SRS710974 SAMN03076578 wAR2 RNA-Seq TRANSCRIPTOMIC RANDOM 200 0 Application Read Forward 1 1 Application Read Reverse 101 Illumina HiSeq 2000 SRX712722 wAR3 SRP048186 Eggs were obtained from natural spawning Solea solea adults. Those fish were grown from juveniles obtained from Solea BV (Ijmuiden, Netherlands) and bred at PFOM fish facility (Ifremer, Brest, France). Fertilised eggs were selected by buoyancy and were put in 60 l incubators at 14°C (water temperature) until hatching. One day post-hatching (dph) larvae were distributed among  cylindrical fibreglass 67 l tanks (5300 larvae per tank). Throughout the experiment, water salinity and oxygenation were maintained at 35‰ and more than 6 mg/l, respectively. Water temperature was progressively increased from 14°C to 16°C and then to 20°C between 1 and 5 dph for acclimation purposes. Embryos at stage 7/8 (gastrula 30 h post fertilisation) were exposed to all-trans RA (ATRA, Sigma-Aldrich, Ref R2625) at final concentration of 10 nM during 3h and collected at 33 h post fertilisation. Samples were washed with DEPC water, frozen in liquid nitrogen and stored at −80 °C until analysis. Pools homogenization was carried out in the Fast-prep FG120 instrument (Bio101) using Lysing Matrix D (Q-Bio- Gene) for 40 s at speed setting 6. Total RNA was isolated from 50 mg of tissues or pools of embryos and larvae using the RNeasy Mini Kit (Qiagen). RNA integrity was further investigated using the Bioanalyzer 2100 (Agilent Technologies) before preparation of library. Illumina libraries were constructed at MGX platform (Montpellier, France) using TruSeq RNA Sample Preparation Kit v2 according to manufacturer’s protocols. Briefly, 0.5 μg of total RNA was used for poly-A based mRNA enrichment selection using oligo-dT magnetic beads followed by fragmentation by divalent cations at elevated temperature resulting into fragments of 80-250 nt, with the major peak at 130 nt. First strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second strand cDNA synthesis performed using RNAseH and DNA Pol I. Double stranded cDNA was end repaired, 3´adenylated and the 3´-“T” nucleotide at the Illumina adaptor was used for the adaptor ligation. The ligation product was amplified with 15 cycles of PCR. Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode 2 x 100 bp in a fraction of a lane (1/7 ) of a HiSeq2000 sequencing system (Illumina, Inc) following the manufacturer’s protocol. SRS710974 SAMN03076578 wAR3 RNA-Seq TRANSCRIPTOMIC RANDOM 200 0 Application Read Forward 1 1 Application Read Reverse 101 Illumina HiSeq 2000