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This dataseries investigates the thermal transcriptome of phytoplankton in response to acute and chronic temperature stress. It is comprised of three subseries: 1. Thermal transcriptome of Phaeodactylum tricornutum in response to gradual heat stress. 2. Thermal transcriptome of Phaeodactylum tricornutum in steady-state growth, and 3. Thermal transcriptome of Synechocystis in response to gradual heat stress. To investigate the molecular underpinnings of gradual heat stress, we expose cultures to high temperature and follow changes in gene expression through time (over a 12 hour period) in comparison to optimal conditions. To understand how the thermal transcriptome response to chronic thermal stress, we acclimated P. tricornutum in steady state growth under optimal conditions and compare the gene expression to that under sub-optimal and supra-optimal conditions. This data is NERC-funded but not held by the EIDC. This data is archived in the Gene Expression Omnibus (GEO) National Center Biotechnology Information (NCBI).