TABLE 1 .

Overview of RNA-Seq libraries used to infer the global regulatory network of P. tricornutum

ID	Experimental conditions	No. of samples	Accession no.
GABA/DD	Exponential growth, diatoms treated with two concentrations of either 2-trans-4-trans-decadienal or γ-aminobutyric acid and sampled over time	44	SAMN05925108–SAMN05925151
CO2	Duplicate cultures at 1,000 and 150 ppm CO2	4	Table S5
CO2 dark/light	Triplicate cultures at 50, 400, and 5,000 ppm CO2 under dark and light conditions	18	SAMN05176215–SAMN05176250
N short term	N-starved cells given different N sources and monitored in the very short term	30	SAMN04488978–SAMN04489007
Pulse-chase	Duplicate culture grown on urea or nitrate and harvested in exponential growth phase	4	SAMN05925158–SAMN05925161
N sources	Cultures grown on 880 μM NO3, 75 μM NO3, 880 μM NH4, 75 μM NH4, 880 μM urea, and 37.5 μM urea; high-nitrogen cultures harvested during exponential growth; low-nitrogen cultures harvested at onset of stationary phase	6	SAMN05925152–SAMN05925157
B12	Cultures grown with or without vitamin B12 at a high or low Fe concentration	8	SRX142057, SRX142058, SRX142055, SRX142059, SRX142060, SRX142061, SRX142086, SRX142087
Fe diel	Cultures grown at 15.0, 30.0, or 300.0 nM total Fe and sampled over a diel cycle	49	SAMN04461541–SAMN04461589
GSA/MSX/Rapa	Experiment examining response to glufosinate, sirolimus, or l-methionine-dl-sulfoximine	16	SAMN05925188–SAMN05925203