RNA-sequencing of A2EN cells infected or not by Chlamydia Trachomatis in presence or in absence of seminal plasma

At different timepoints and for different conditions, A2EN cells were lysed and processed for RNA extraction, processing and sequencing (Oxford Nanopore Technologies, Oxford, UK). Samples were quantified then loaded on R9.4.1 Flow cells using GridION instrument. Sequence reads were converted into FASTQ files. Reads under 300 bp or with a quality score under 9 were discarded. The remaining reads were aligned on the human GRCh38.p13 and C. trachomatis D/UW-3/CX strain transcriptome of reference (GeneBank assembly accession numbers GCA_000001405 and GCA_000008725 respectively) using minimap2 version 2.24. To quantify transcripts, the resulting alignments were given to Salmon version 1.8.0. To explore differentially expressed genes, replicates count data were used on DESeq2 version 1.32.0 in one single DEseq model. Gene set enrichment analysis with both upregulated and downregulated genes Log2FC>1.5 or Log2FC<1.5, respectively was performed using Enrichr, a web server enrichment analysis tool, and BioPlanet 2019 database for cellular and signaling pathway analysis.