GSM7440261: Primary mouse SHH MB SOX2+ tumor cells replicate 1; Mus musculus; ATAC-seq
After sorting, live cells were collected into 0.1%BSA/PBS. 35,000 – 50,000 cells were collected, depending on sample viability. Equal numbers of GFP+ and GFP-  or RFP+ and RFP- cells were used for downstream ATAC protocol. Each sample was washed in PBS and centrifuged at 600g for 10 minutes. Cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630, 0.1% tween) was used to lyse cells and the nuclei were immediately spun down at 600g for 10 minutes at 4°C. Following nuclei prep, the pellets were resuspended in a transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water) for 30 minutes at 37°C. Following transposition, the samples were purified using Qiagen MinElute Kit. Next, library fragments were amplified using the NEBNext High Fidelity 2X PCR Master MixEndFragment (NEB) and the libraries were purified using a Qiagen MinElute Kit. Following purification, the libraries were selected for 100-600bp size range using Pippin Prep (Sage Science). The resulting libraries were controlled for quality by qPCR. ATAC-seq libraries passing QC were sequenced on an Illumina HiSeq 2500 platform, using a Rapid Run mode flow cell to generate 50 bp single-end reads.