Transcriptome of Coxiella burnetii infected Human Macrophages

PMA-differentiated THP1 cells were infected with NMII or DotA strains of Coxiella burnetii and were analyzed at 8h, 24h, 48h, 72h, and 120h post-infection for mRNA and microRNA expressions. Both bulk and single-cell RNA sequencing (10X Genomics single-cell 3' v3) of NMII-infected, bystander, and uninfected THP-1 cells were performed to gain a deeper insight at 48h post-infection. Moreover, primary human alveolar macrophages (hAMs) obtained from postmortem human donor lungs were infected with Coxiella burnetii NMI, NMII, Dugway, or Graves strains and analyzed at 72h post-infection. Each sample contained three biological replicates for bulk RNA-Seq and total RNA extraction was done using TRI reagent followed by DNase treatment. Libraries were prepared after miRNA enrichment for the respective samples and rRNA removal using a RiboZero kit with a TruSeq RNA sample preparation kit. Samples were sequenced under the Illumina platform at Yale Center for Genome Analysis, New Haven, CT, or Novogene Corporation, Sacramento, CA.