GSM3664756: KO1_LT_HSC_ATAC-Seq; Mus musculus; ATAC-seq
Total RNA was prepared using RNeasy Micro Kit (Qiagen) according to manufacturer's instructions. mRNA was enriched by using oligo dT magnetic beads for library preparation. Assays for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) were performed as described before (Buenrostro et al., 2015). To prepare nuclei, 10.000 cells were resuspended in 50 µL of cold lysis buffer (10 mM Tris•Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% [v/v] Igepal CA-630) and incubated for 15 min on ice. The supernatant was discarded after centrifugation, and the nuclei were used for transposition reaction immediately. The RNA-seq libraries were prepared by using SMART-Seq v4 ultra-low input RNA library preparation protocol according to the manufacturer's instructions. The ATAC-seq libraries were prepared using the NEB Nextera DNA sample preparation kit according to the manufacturer's instructions.