title: GSM6368753: Bulk ATAC-seq Yy1_KO/Ngn2+ rep2; Mus musculus; OTHER
library_construction_protocol: The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 5 days, the astrocytes were infected with a lentivirus which constitutively expressed the Cre protein and tdTomato fluorescent protein. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct, which expressed Ngn2. The Ngn2 expressing lentiviral construct was induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement. After 48 hours of doxycycline induction, the cells were harvested and FACS sorted based on the experimental conditions: Yy1_WT (RFP+), Yy1_KO (RFP+), Yy1_WT/Ngn2+ (GFP+), Yy1_KO/Ngn2+ (GFP+RFP+) Directly after FACS isolation, the nuclei of 10,000 cells were transposed with a modified Tn5 transposase (Illumina Tagment DNA TDE1 Enzyme and Buffer kit, 20034198) according to the OMNI-ATAC-seq protocol (Corces et al., 2017), the trasposed DNA was isolated using the DNA clean and concentrator kit from Zymo Research (D4014) and the ATAC-seql ibraries were prepared using NEBNext Ultra II  Q5 Master mix  from NEB (M0544S) according to manufacturer's instructions. The size distribution of the ATAC-seq libraries was analysed using an Agilent 2100 Bioanalyser. The ATAC libraries were sequenced to a depth of 50 million reads (paired-end)