RAW-Control
The RAW-Control and RAW-Ipr1 cells were infected with H37Ra (MOI = 5) for 24 h (named RAW-Control (+H37Ra) and RAW-Ipr1 (+H37Ra) respectively), and uninfected RAW-Control and RAW-Ipr1 cells were used as controls. Three independent experiments were performed to prepare each sample. The total RNA was isolated using Trizol reagent (Invitrogen). RNA integrity was checked by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA). For each sample, equal amounts of total RNA from three independent experiments were pooled. For RNA-seq, the total RNA samples were treated with DNase I to degrade any possible DNA contamination. Then the mRNA was enriched using the oligo (dT) magnetic beads from the total RNA and then mixed with the fragmentation buffer, and the mRNA was fragmented into short fragments (about 200 bp) followed by synthesized of first strand of cDNA using random hexamer-primer. The second strand was subsequently  synthesized. The double-strand cDNA was purified with magnetic beads, and the end reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The resulting fragments were enriched by PCR amplification. For small RNA sequencing, the sRNA (18 to 30 nt) was gel purified and ligated to the 3' and 5' adaptor. The ligated products were reverse transcribed, followed by acrylamide gel purification and PCR amplification to generate sRNA libraries as previous described.