A primary T. gondii GT1 strain was subjected to lab adaptation by serial in vitro passages for over 250 passages. Extracellular survival was the strongest selection pressure over lab adaptaion. The lab adaptation was mainly driven by transcriptional changes. RNA and ATAC sequencing on lab-adaptation passages and applying several computational methods revealed up and down trending clusters of genes. Analysis of trending genes revealed a significant overlap with the bradyzoite differentiation transcriptome, indicating that shared stress pathways are involved in both situations. Moreover, significan overlap between the transcription factors driving the transcriptional of the lab adapting extracellular parasites and bradyzoite differentiation program coroborates the hypothises of shared stress mechanism between extracellular lab adaptatioin and bradyzoite differentitaion.
- peak gene assignment
- RNA-seq processing
- ATAC-seq processing
- RNA-seq clustering
- ATAC-seq clustering