GSM8573303: ATAC-seq, hatchling, whole animal, sample 2; Paraspadella gotoi; ATAC-seq
ATAC-seq was performed following the Omni-ATAC protocol using Digitonin (Promega) in addition to NP40 and Tween in the cell lysis buffer  (Corces et al., 2017). Sea urchin eggs were fertilised in filtered sea water with 2 mM of Paraminobenzoic acid (Sigma) to prevent hardening of the fertilisation envelope. The fertilization envelope was then removed by repeated filtration on a nylon net (70 µM). Embryos at the appropriate stage were collected and washed in NaCl 0,55M twice then dissociated in Calcium-Magnesium artificial sea water by energetic pipetting. For each time point, different numbers of nuclei were tested, typically 50,000, 150,000 and 250,000. The integrity of the nuclei was checked on a microscope after staining the nuclei with Hoechst. After tagmentation the libraries were purified with a Zymo DNA clean up kit then a QPCR was performed on an aliquot  of the eluted libraries using the Ad1 and Ad2.x primers and the corresponding Ct was determined for each sample (Buenrostro et al. 2013). The libraries were then amplified at Ct+ 2 cycles. The quality of the libraries was checked on a 2% agarose gel to verify the size of the fragments and the nucleosome phasing.