title: GSM4890003: E10.5 mouse embryonic maxillary prominence mesenchymal cells_sample3-rep2; Mus musculus; ATAC-seq
library_construction_protocol: Maxillary mesenchyme was separated from maxillary ectoderm using a protocol described previously (Hong Li et al., Journal of Visualized Experiments, 2013). 10 mg/ml Dispase II (Roche, Cat# 4942078001) in Hepes-buffered Saline (HBS) (50 mM Hepes/KOH pH 7.4, 150 mM NaCl) was prepared freshly and diluted 1:10 in PBS right before use. Dissected embryos were treated with 1 mg/ml Dispase II at 37 °C for 30 min. Maxillary prominences were then dissected out and pipetted up and down 5 times using a long glass pasture pipette. Maxillary ectoderm was peeled off from maxillary prominences very slowly using forceps to minimize disruption of tissue structure. The mesenchyme samples were washed with PBS and centrifuged at 4 °C, 800 x g for 5 min. Around 50,000 freshly prepared maxillary mesenchyme cells were used for each ATAC-Seq library preparation. The cells were lysed in 1 × Lysis Buffer (10mM Tris-HCl(pH7.4),10mM NaCl, 3mM MgCl2, 0.5% NP-40) to get the nuclei, and TruePrepTM DNA Library Prep Kit V2 for Illumina (Vazyme Biotech, TD501) was used to construct the transposase-treated libraries. Libraries were amplified for 5-9 PCR cycles and size selected using VAHTS DNA Clean Beads (Vazyme Biotech, N411-01-AA). The mass concentration and molar concentration of libraries were assessed by Qubit 3.0 Fluorometer and StepOnePlusTM Real-Time PCR system, respectively, and lengths of inserted fragments were detected with Agilent HS 2100 Bioanalyzer. Qualified libraries were sequencing on an Illumina HiSeq X ten platform under pair-end 150 bp mode.