GSM9151892: H3K4me3_CT_mESC_Gabpa_1h_DMSO_rep1; Mus musculus; OTHER
For RNA-seq, RNA was isolated with TRIzol. For SLAM-seq, the 4sU-labeled RNA was isolated using a 1:1 volume of RNA XP magnetic beads. After 10 mins incubation at room temperature, the beads were washed twice with 200 μL 80% freshly prepared ethanol on the magnetic stand and the dried beads pellets were resuspended in 7 μL RNase-free water. For ATAC-seq and CUT&Tag, DNA was purified using the SPRI beads. For RNA-seq, libraries were prepared according to the Fast RNA-seq Lib Prep Kit V2 with 0.2 μg RNA following the manufacturer's protocols. For SLAM-seq, alkylated RNA was used for 3'-end polyA RNA sequencing library preparation with Smart-seq2 according to the manufacturer's protocol. For ATAC-seq, mESCs cells were digested with adapter-loaded Tn5 in the tagmentation buffer (33 mM Tris-Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate,16% DMF, 0.02% Digitonin) for 30 mins at 37 °C, and the reaction was stopped by stop buffer (100 mM Tris pH 8.0, 100 mM NaCl, 0.4% SDS and 40 μg/mL Proteinase K) and incubated overnight at 55 °C. 25% Tween-20 was added to quench SDS. Sequencing libraries were prepared with NEBNext High-Fidelity 2x PCR Master Mix. The PCR product was purified using a 1:1.6 volume ratio of SPRI beads. For CUT&Tag, libraries were performed using the Hyperactive Universal CUT&Tag Assay Kit following the manufacturer's protocols.