Protocols: FACS sorting were performed as previously described (Torres-Mendez et al. 2019). Briefly, animals were dissociated in 0.25% Trypsin (Gibco, 27250018) in Ca- Mg- free Nematostella media (CMFNM) (154 mM NaCl, 3.6 mM KCl, 2.4 mM Na2SO4, 0.7 mM NaHCO3) supplemented with 6.6 mM EDTA , pH 7.6-7.8. Cells were centrifuged at 800 g for 10 minutes, resuspended in ice cold 0.5% BSA in CMFNM (pH 7.6-7.8), filtered through a 40 μM filter and stained with Hoechst 33342 (Thermo Fisher Scientific, 62249) at a 60 μg/ml at RT for 30 minutes. Samples were then diluted 1:1 with ice cold 0.5% BSA/CMFNM and stained with 60 μl/ml 7-AAD (BD, 559925) for > 20 minutes on ice. Sorting was carried out on a BD FACSAria II with a 100 μm nozzle. RNA extraction was performed as previously published (Torres-Mendez et al. 2019). Cells were sorted directly into 0.5% BSA/ CMFNM at 4°C and centrifuged at 800 g for 10 minutes at 4°C. Most of the liquid was removed and 3 volumes of TRIzol LS reagent (Invitrogen, 10296028) was added. Samples were vortexed extensively and incubated at RT for 5 minutes before being flash frozen and stored at -80°C. The samples were processed using Direct-zol RNA MicroPrep columns (Zymo Research, R2060) including on column DNase digestion. cDNA was prepared from 400 pg of total RNA using the Smart-Seq 2 method with 16 pre-amplification PCR cycles (Picelli et al. 2014). NGS libraries were prepared using the home-made tagmentation-based method (Hennig et al. 2018). Briefly, 125 ng of cDNA was tagmented using home-made Tn5 loaded with annealed linker oligonucleotides for 3 minutes at 55°C. Reactions were inactivated by adding 1.25 ml of 0.2% SDS and incubation for 5 minutes at RT. Indexing and amplification was done using the KAPA HiFi HotStart PCR kit (Sigma-Aldrich, KK1508) with Index oligonucleotides (sequences were adapted from Illumina).