SE193:/S1/M3/D1

Sample Set Information

ID	TSE1352
Title	Metabolic Reprogramming in Leaf Lettuce Grown Under Different Light Quality and Intensity Conditions Using Narrow-Band LEDs
Description	Light-emitting diodes (LEDs) are an artificial light source used in closed-type plant factories and provide a promising solution for a year-round supply of green leafy vegetables, such as lettuce (Lactuca sativa L.). Obtaining high-quality seedlings using controlled irradiation from LEDs is critical, as the seedling health affects the growth and yield of leaf lettuce after transplantation. Because key molecular pathways underlying plant responses to a specific light quality and intensity remain poorly characterised, we used a multi-omics–based approach to evaluate the metabolic and transcriptional reprogramming of leaf lettuce seedlings grown under narrow-band LED lighting. Four types of monochromatic LEDs (one blue, two green and one red) and white fluorescent light (control) were used at low and high intensities (100 and 300 μmol·m−2·s−1, respectively). Multi-platform mass spectrometry-based metabolomics and RNA-Seq were used to determine changes in the metabolome and transcriptome of lettuce plants in response to different light qualities and intensities. Metabolic pathway analysis revealed distinct regulatory mechanisms involved in flavonoid and phenylpropanoid biosynthetic pathways under blue and green wavelengths. Taken together, these data suggest that the energy transmitted by green light is effective in creating a balance between biomass production and the production of secondary metabolites involved in plant defence.
Authors	Kazuyoshi Kitazaki, Atsushi Fukushima, Ryo Nakabayashi, Yozo Okazaki, Makoto Kobayashi, Tetsuya Mori, Tomoko Nishizawa, Sebastian Reyes-Chin-Wo, Richard W. Michelmore, Kazuki Saito, Kazuhiro Shoji & Miyako Kusano
Reference	Scientific Reports, volume 8, Article number: 7914 (2018)
Comment

www.nature.com/articles/s41598-018-25686-0

Sample Information

ID	S1
Title	red leaf lettuce
Organism - Scientific Name	Lactuca sativa L.
Organism - ID	NCBI:txid4236
Compound - ID
Compound - Source
Preparation	BioSource Species Lactuca sativa L. Genotypes/Varieties cv. Banchu Red Fire Organ specification The third leaf Growth conditions Under white fluorescent light (FL, FLR110H-W1A; Mitsubishi/Osram Co.; Yokohama, Japan), seeds of red-leaf lettuce (Lactuca sativa L. cv Banchu red fire; Takii seed, Kyoto, Japan) were pregerminated [14 hr, 14 days, 23 ± 2ºC, 100 µmol m−2 s−1 photon synthetic photon flux density (PPFD)]. The seedlings were supplied with a nutrient solution (Otsuka hydroponic composition, Otsuka Chemical Co. Ltd., Osaka, Japan) adjusted to an electrical conductivity (EC) of 1.2 dS/m and pH 5.8. It contained 7.0 mmol l-1 NO3-, 0.6 mmol l-1 NH4+, 3.7 mmol l-1 K+, 2.3 mmol l-1 Ca2+, 1.3 mmol l-1 H2PO4-, and 0.9 mmol l-1 Mg2+. The seedlings were transplanted to cultivation panels in a growth chamber (VB1514; Vötsch, Germany), supplied with nutrient solution for the duration of the experiments, and grown at 25ºC [relative humidity (RH) 60%, 900 µmol mol-1 CO2]. The plants were irradiated with different light spectra from LEDs, namely B470 (peak wavelength 470 nm, ISL305X302-BBBB, CCS Co., Kyoto, Japan), G510 (peak wavelength 510 nm, ISL-305X302- GGGG505, CCS Co.), G520 (peak wavelength of 524 nm; ISL-305X302-GGGG525, CCS) and R680 (peak wavelength of 680nm; ISL-305X302-RRRR68, CCS Co., Kyoto, Japan). The seedlings were irradiated for 24 hr at PPFD 100 or 300 µmol m−2 s−1 (P100, P300). The wavelength of the light source was determined with a USB2000 spectrometer (Ocean Optics, Dunedin, FL, USA). At 14, 15 and 21 DAS, dry weight (DW) was measured.
Sample Preparation Details ID
Comment

Analytical Method Information

ID	M3
Title	LC-q-TOF-MS (to detect lipids)
Method Details ID	MS3
Sample Amount	1 μL
Comment

Analytical Method Details Information

ID	MS3
Title	LC-q-TOF-MS (to detect lipids)
Instrument	LC, Waters Acquity UPLC system; MS, Waters Xevo G2 Q-Tof
Instrument Type	UPLC-QTOF-MS
Ionization	ESI
Ion Mode	positive and negative
Description	Extraction for LC-q-TOF-MS to detect lipids Each frozen sample was milled using mixer mill MM301 (Retsch) at a frequency of 20 Hz for 2 min at 4°C. After that, frozen powder was extracted with 20 fold volume of extraction solvent (chloroform/methanol/water[50 : 100 : 31.45, v/v]) containing 1 µM of 1,2-didecanoyl-sn-glycero-3- phosphocholine (SIGMA). Samples were vigorously mixed using a vortex mixture. 52.6 µl of water and 52.6 µl of chloroform were added to 200 µl of extract and then vigorously mixed for 5 min at room temperature. After standing for 15 min on ice, the samples were centrifuged at 1,000 ×g at 5°C for 5 min. The lower layer (85 µl) was transferred to a 2 ml tube. Each extract was evaporated to dryness by SPD2010 SpeedVac® concentrator (Thermo Fisher Scientific). The residue was dissolved in 162 µl of ethanol, and centrifuged at 10,000×g at 5°C for 15 min. The supernatant was transferred to a glass insert and subjected to lipid analysis by LC-MS. LC-q-TOF-MS conditions to detect lipids Sample extracts (1 µl) were analyzed using an LC-MS system equipped with an electrospray ionization (ESI) interface (HPLC, Waters Acquity UPLC system; MS, Waters Xevo G2 Qtof). Twosolvent (A and B) system was used for separation of each metabolite. Compositions of these solvents were as follows: solvent A, acetonitrile: water:1 M ammonium acetate:formic acid = (158 g:800g:10 ml:1 ml); solvent B, acetonitrile:2-propanol:water:1 M ammonium acetate:formic acid = (79 g:711 g:10 ml:1 ml). The analytical conditions were as follows. HPLC: column, Acquity UPLC HSS T3 (pore size 1.8 µm, 1.0 i.d × 50 mm long, Waters); gradient program, 35% B at 0 min, 70% B at 3 min, 85% B at 7 min, 90% B at 10 min, 90% B at 12 min and 35% B at 12.5 min; flow rate, 0.15 ml/min; temperature, 55°C; MS detection: capillary voltage, +3.0 kV; cone voltage, 20 V for positive mode and 40 V for negative mode; source temperature, 120°C; desolvation temperature, 450°C; cone gas flow, 50 l/h; desolvation gas flow, 450 l/h; collision energy, 6 V; detection mode, scan (m/z 100–2000; scan time, 0. 5 sec; centroid). The scans were repeated for 15 min in a single run. The data were recorded using MassLynx version 4.1 software (Waters).
Comment_of_details

Data Analysis Information

ID	D1
Title	Data processing for LC-q-TOF-MS data to detect lipids
Data Analysis Details ID	DS3
Recommended decimal places of m/z
Comment

Data Analysis Details Information

ID	DS3
Title	Data processing for LC-q-TOF-MS data to detect lipids
Description	The data matrix was generated using the Makerlynx XS (Waters) using the profiling data files recorded in the MassLynx format (raw). The data matrices were processed using in-house Perl script. The original peak intensity values were divided with that of the internal standard (1,2-didecanoyl-snglycero-3-phosphocholine at m/z 566.382 [M + H]+ and at m/z 610.372 [M + HCOO]– for the positive and negative ion modes, respectively) to normalize the peak intensity values among the metabolic profile data.
Comment_of_details