title: CT/CM Half PZ chimera R2
design: PZ chimeric strains and their parents were grown in L929 cells at a MOI of 5. At 20 hpi, the infections were harvested for RNA using TRIzol (Invitrogen). RNA was purified by phenol/chloroform extraction followed by DNase treatment with TURBO DNase (Invitrogen). Residual DNA contamination was assessed by converting a portion of the RNA into cDNA using the High-Capacity cDNA Reverse Transcription Kit (Thermo Fisher), with control reactions containing no reverse transcriptase, and performing PCR on cDNA reactions. Ribosomal RNA was then depleted using NEBNext rRNA Depletion (Human/Mouse/Rat) (New England Biosciences) and RiboMinus Transcriptome Isolation bacterial (Invitrogen) kits. A final purification step was performed using the RNeasy Mini kit (Qiagen). rRNA depletion was assess by running samples on a 2% agarose gel. RNA quality was assessed using Qubit quantification and TapeStation gel analysis. Library prep for RNAseq was performed using NEBNext Standard mRNA library kit without the polyA selection step. Sequencing was performed on the NextSeq550 with single read 50bp read length. Geneious Prime (Version 2019.1.1) was used for the data analysis. Reads were aligned to Chlamydia muridarum Nigg (NC002620) and/or Chlamydia trachomatis tet9 (CP035484.1).