GSE129949
Whole transcriptome profiling of static and suspension-cultured schizonts of the P. falciparum strains W2mef and Dd2.
Overview: RNA-seq was used to profile the whole-transcriptome gene expression of highly replicated schizont-stage cultures of W2mef and Dd2 grown under static and suspended conditions. Methods: Transcript profiles of schizont stages of static and suspended W2mef and Dd2 were generated by RNA sequencing. Two to eight replicates were sequenced per sample. Illumina stranded TruSeq libraries were sequenced using an Illumina MiSeq. Hisat2 was used to align paired-end fastQ files and indexed bam files generated with samtools. Bam files were filtered to exclude reads with MAPQ scores below 60, reads counted using the SummarizeOverlaps feature of the GenomicAlignments package in R and differential expression analysis conducted using DESeq2 in R. Results: We show that in addition to invasion-related genes, parasites that have been induced to switch invasion phenotype upon culturing in suspension increase the expression of a number of genes most of which belong to gene families that code for exported proteins. Conclusions: Our data suggest that in addition to invasion phenotype switch, suspension cultures may select for other parasite properties that may be essential for parasite survival in vivo. Overall design: TruSeq stranded mRNA libraries of two to eight schizont-stage replicates of static and suspended W2mef and Dd2 were sequenced using an Illumina MiSeq.