GSM4979670: Input-WT_LPS-6H-rep2; Mus musculus; ChIP-Seq
For histone ChIP-seq, lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with H3K4me1,H3K4me3 or H3K27Ac antibodies. For p300 and Hdac3 ChIP-seq, lysates were clarified from sonicated nuclei and p300-DNA or Hdac-DNA complexes were isolated with p300 or Hdac3 antibodies. Illumina libraries were constructed using a modified custom paired-end protocol. In brief, samples were end-repaired (1*T4 DNA ligase buffer, 0.4 mM dNTP mix, 2.25 U T4 DNA polymerase, 0.75 U Klenow DNA polymerase and 7.5 U T4 polynucleotide kinase; 30 min at 21–25 C), A-tailed (1*NEB buffer 2, 0.4 mM dNTPs and 3.75 U of Klenow (exo-); 30 min at 37 C) and ligated (1*rapid DNA ligation buffer, 1 mM Illumina PE adapters and 1,600 U DNA ligase; 1–8 h at 21–25 C). Ligated fragments were amplified using indexed primers (Illumina) for 8–12 PCR cycles. DNA was purified with 1.8 volume KAPA DNA purification beads between each step.