title: GSM6927722: ATAC_Flx2: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep2; Mus musculus; ATAC-seq
library_construction_protocol: For ATAC-seq, 106 primary cortical neurons plated on a 35 mm dish were washed twice with 1X PBS before addition of nuclei isolation buffer (1X PBS, 0.1 % Triton X-100, 5 mM AEBSF Pefabloc, 5 mM Na-Butyrate, 1 tablet cOmplete EDTA-free Protease inhibitor). The dish was incubated on a shaker at 4°C for 7 min before detaching the cells with a cell lifter and gently resuspending them. Cell suspension was spun down at 500 g at 4 °C for 10 min. Supernatant was removed and pellet was gently resuspended in 1X PBS with protease inhibitors. Intact nuclei were counted in a Neubauer chamber. 25 000 nuclei were used for tagmentation in 4X TD buffer (132 mM Tris-acetate pH 7.8, 264 mM Potassium-acetate, 40 mM Magnesium Acetate, 64 % Dimethylformamide, 0.005 % Digitonin and 1.5 µl Tn5 Transposase (15027865 Illumina)). Reaction was incubated at 37 °C for 30 min and purified using the QIAGEN MinElute Kit (28004 QIAGEN) according to the manufacturers protocol. Each library was given a unique barcode and amplified for 11 cycles. Afterwards, the PCR reaction was purified using 1X AMPURE XP Beads and eluted in 33 µl of 10 mM Tris HCl pH 8.0. Libraries were analyzed with Qubit and fragment size was accessed using the high sensitivity D-5000 screen tapes (5067-5592 Agilent) on a Tapestation.