GSM7050285: 6 month old Ts65Dn mouse model for down syndrome, biological rep 2 (snATAC-seq); Mus musculus; ATAC-seq
Frozen tissue was thawed in 500 uL Buffer HB (0.25M sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH pH 7.8, 0.15mM spermine tetrahydrochloride, 0.5mM spermidine trihydrochloride, 1mM DTT). The tissue was transferred to a 2 mL dounce. 500ul 5% IGEPAL CA-630 (Sigma) and 1 mL HB were added to the tissue and the tissue was homogenized with a tight pestle 10-15 times. The sample was transferred to a 15 mL tube and total solution brought to 9 mL with HB. In a ultra-clear centrifuge tubes (Beckman Coulter), 1 mL 30% iodixanol layered on top of 1 mL 40% iodixanol. The 9 mL sample was layered on top of the iodixanol cushion. The sample was spun at 10,000 xg for 18 minutes. 1 mL of sample at the 30-40% iodixanol interface was collected for subsequent nuclei processing. The snRNAseq and snATACseq libraries were constructed and sequenced as described in the 10X Genomics protocol.