Gastrula_Nvectensis_scATAC-seq v1

This protocol describes the steps for isolating single nuclei from gastrula-stage embryos of the cnidarian Nematostella vectensis for scATAC-seq using 10x Chromium platform. Nuclei are directly isolated and permeabilized by mechanically dissociating gastrula embryos in hypotonic OmniATAC lysis buffer1 supplemented with 70µM Pitstop2 to increase nucleus permeability to Tn52. After washing, nuclei are visually inspected under the microscope, counted, and tagmented in bulk prior to single-nucleus encapsulation using 10x Chromium platform. scATAC-seq libraries are then prepared according to manufacturer`s instructions.