RNA-seq transcriptomes of Micromonas commoda under DMSP and vitamin B12 treatments across growth phases and light conditions
In this work, transcriptomic responses of the marine microalga Micromonas commoda RCC299 were investigated under controlled laboratory conditions across two independent experiments conducted in July 2021 and December 2023. The second experiment was conducted to complement the initial dataset by recovering a missing sampling condition (mid-exponential phase under light conditions, hereafter referred to as expo/light) and increasing replication for specific conditions. Cultures were grown in duplicate under standard conditions and subjected to different nutrient treatments to the growth medium: (i) without any compound additions (Control); (ii) daily additions of 0.5 µM dimethylsulfoniopropionate (+DMSP); (iii) daily additions of 0.2 nM vitamin B12 (+B12); and (iv) a combined DMSP and B12 treatment as describe above (+DMSP+B12). The (iv) was included in the second experiment only. Samples were collected at two growth stages: mid-exponential phase (expo) and early stationary phase (stat), and under both dark (end of night) and light (one hour after light onset) conditions. This resulted in four sampling conditions: expo/dark, expo/light, stat/dark, and stat/light. For RNA extraction, 25–50 mL of culture were filtered onto 0.2 µm pore-size polycarbonate filters (47 mm diameter), flash-frozen in liquid nitrogen, and stored at -80°C. Filters were mechanically disrupted using bead beating (PowerSoil beads, MoBio), and total RNA was extracted using the RNeasy Mini Kit (Qiagen). Residual DNA was removed using the TURBO DNA-free Kit (Ambion), followed by ethanol precipitation and resuspension in Tris-HCl buffer. Library preparation and sequencing were performed by Sequentia Biotech. Ribodepletion, RNA fragmentation, and reverse transcription were carried out using the TruSeq Stranded mRNA protocol (Illumina). Sequencing was conducted on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads, generating approximately 7.5–18 Gb per sample.
In this work, transcriptomic responses of the marine microalga Micromonas commoda RCC299 were investigated under controlled laboratory conditions across two independent experiments conducted in July 2021 and December 2023. The second experiment was conducted to complement the initial dataset by recovering a missing sampling condition (mid-exponential phase under light conditions, hereafter referred to as expo/light) and increasing replication for specific conditions. Cultures were grown in duplicate under standard conditions and subjected to different nutrient treatments to the growth medium: (i) without any compound additions (Control); (ii) daily additions of 0.5 µM dimethylsulfoniopropionate (+DMSP); (iii) daily additions of 0.2 nM vitamin B12 (+B12); and (iv) a combined DMSP and B12 treatment as describe above (+DMSP+B12). The (iv) was included in the second experiment only. Samples were collected at two growth stages: mid-exponential phase (expo) and early stationary phase (stat), and under both dark (end of night) and light (one hour after light onset) conditions. This resulted in four sampling conditions: expo/dark, expo/light, stat/dark, and stat/light. For RNA extraction, 25–50 mL of culture were filtered onto 0.2 µm pore-size polycarbonate filters (47 mm diameter), flash-frozen in liquid nitrogen, and stored at -80°C. Filters were mechanically disrupted using bead beating (PowerSoil beads, MoBio), and total RNA was extracted using the RNeasy Mini Kit (Qiagen). Residual DNA was removed using the TURBO DNA-free Kit (Ambion), followed by ethanol precipitation and resuspension in Tris-HCl buffer. Library preparation and sequencing were performed by Sequentia Biotech. Ribodepletion, RNA fragmentation, and reverse transcription were carried out using the TruSeq Stranded mRNA protocol (Illumina). Sequencing was conducted on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads, generating approximately 7.5–18 Gb per sample.
INSTITUT DE CIENCIES DEL MAR