title: RNA-seq of Chlamydomonas reinhardtii: Agar   Dark
design: For agar-grown samples, colonies were frozen at -80 C before RNA extraction. RNA was isolated from individual colonies using RNeasy Qiagen plant kit. For liquid-grown samples, 1.5x107 cells were pelleted for RNA extraction at time point 12h and 5.5x107 cells at time point 28h. RNA was extracted according to (16). RNA samples were quantified by Ribogreen and those passing the quality control (Bioanalyzer, Agilent technologies, Agilent 2100 Expert software) were selected for cDNA synthesis. Library preparation started with 100 ng total RNA for agar-grown samples 500 ng total RNA for liquid-grown samples. Illumina Sequencing (PE 1x75 on a NextSeq500 machine) was performed at the GIGA-R Sequencing platform (University of Li ge) following manufacturer s protocol (Illumina Inc, San Diego CA, USA).