input (treated with LPS)
Cells were stimulated with lipopolysaccharide for 3 hours. Cross-linking was with 1% formaldehyde. Cell disruption was with Dounce homogenization. Nuclear preparations were digested with micrococcal nuclease. Nucleic acid was prepared with phenol/chloroform extraction. DNA was removed by digestion with RNase-free DNase. The library was constructed using the Illunmina Truseq small RNA preparation protocol.