GSM8489272: Control (PBS treated) Embryonic day 12.5 female biological rep 2; Mus musculus; ATAC-seq
Frozen tissue was thawed in 1 ml buffer HB (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 0.15 mM spermine tetrahydrochloride, 0.5 mM spermidine trihydrochloride, 1 mM DTT). The samples were dounced in HB and 5% IGEPAL CA-630 (Sigma-Aldrich) and equal volume of 50% iodixanol was added. 1 ml 30% iodixanol was layered on top of 1 ml 40% iodixanol in a Corex tube (ThermoFisher). The sample was layered on top of the 30% iodixanol and ultra-centrifuged at 7600 × g for 18 min at 4C. Nuclei were collected from the interface of 30–40% iodixanol. Nuclei were processed for scATAC-seq using 10X Genomics standard protocols.