GSM4202168: Banf1 WT H3K27ac ChIP-seq; Mus musculus; ChIP-Seq
For RNA-Seq, total RNA from 10^6 control BV2 cells, Banf1 gene-edited cells, and Banf1-complemented cells were extracted using RNeasy Mini Kit (Qiagen).   For native ChIP-Seq, aliquots of 10^5 cells were suspended in 20 µl of EZ nuclei isolation buffer (Sigma) and digested using 20 µl MNase (NEB MNase buffer, 1 µl MNase, and 3 mM DTT) for 5 min at 37°C, which was quenched by addition of 4.4 µl of 100 mM EDTA, and 4.4 µl of 1% Triton X-100 and 1% deoxycholate. Digested nucleosomes were diluted in complete ChIP immunoprecipitation buffer (20 mM Tris-HCL pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 5 mM sodium butyrate, and protease inhibitors (Roche)), precleared using Dynabeads (Invitrogen) for 1 h at 4°C, and subjected to immunoprecipitation overnight at 4°C (0.1 µg H3K27ac, Abcam, ab4729). Bead chromatin complexes were washed sequentially using low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl) and high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 500 mM NaCl) and then eluted with 1% SDS and 100 mM NaHCO3 for 1 h at 65°C. DNA was purified using Maxtract tubes (QIAGEN) and precipitated overnight. The quality of the RNA samples was evaluated using Bioanalyzer 2100 (Agilent) and prepared using mRNA ribo-deplete. Libraries were sequenced on Illumina HiSeq2500 platforms (Genome Technology Access Center, Washington University).
GEO Accession
GSM4202168