LPS-treaetd M1 cells are firstly fixed in 1% final concentration of formaldehyde for 10 minutes. For mtDNA ChIP-seq, mitochondria are purified from the formaldehyde fixed cells. In both case, ChIP-isolated DNA fragments are carried out using the ChIP Assay Kit (Millipore # 17-295). Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired and blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hi-Seq following the manufacturer's protocols.sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.