ena-STUDY-IMPERIAL COLLEGE-12-03-2021-16:36:23:803-1746
We performed Dual (host and pathogen) RNA-sequencing on whole blood of C57BL/6 mice infected with Plasmodium berghei ANKA, Plasmodium berghei NK65, Plasmodium yoelii 17XL, Plasmodium yoelii 17XNL, or Plasmodium chabaudi AS at their respective early and late stage of infection.
Animal models are widely used to assist the study of human disease, but it is often challenging to quantify how well they reproduce the pathogenesis of the disease in humans. The relevance of mouse models has been particularly controversial in severe malaria research. We performed Dual (host and pathogen) RNA-sequencing on whole blood of C57BL/6 mice infected with Plasmodium berghei ANKA, Plasmodium berghei NK65, Plasmodium yoelii 17XL, Plasmodium yoelii 17XNL, or Plasmodium chabaudi AS at their mouse-model specific respective early and late stage of infection. Libraries were prepared from 1µg of total RNA with the use of ScriptSeq v2 RNA-seq library preparation kit (Illumina) and the Globin-Zero Gold kit (Epicentre) to remove globin mRNA and ribosomal RNA. Prepared strand-specific libraries were sequenced using the 2x125bp protocol on an Illumina HiSeq 2500 instrument. 6 samples were selected for RNA-Sequencing from each infection (3 from the early time point and 3 from the late time point), along with 3 uninfected control samples. The early stage is when the first malaria symptoms were observed. The late stage is defined as the models peak severity (humane endpoint). These mouse models were then compared to a number of publically available human malaria, both RNA-Seq and microarray, datasets to identify the mouse model(s) that best resembles different human manifestations of this disease at the transcriptomic level (comparative transcriptomics). The insert size has been set to 0 for all paired end sample fastq files because these are unknown. The read length is 125bp.
Animal models are widely used to assist the study of human disease, but it is often challenging to quantify how well they reproduce the pathogenesis of the disease in humans. The relevance of mouse models has been particularly controversial in severe malaria research. We performed Dual (host and pathogen) RNA-sequencing on whole blood of C57BL/6 mice infected with Plasmodium berghei ANKA, Plasmodium berghei NK65, Plasmodium yoelii 17XL, Plasmodium yoelii 17XNL, or Plasmodium chabaudi AS at their mouse-model specific respective early and late stage of infection. Libraries were prepared from 1µg of total RNA with the use of ScriptSeq v2 RNA-seq library preparation kit (Illumina) and the Globin-Zero Gold kit (Epicentre) to remove globin mRNA and ribosomal RNA. Prepared strand-specific libraries were sequenced using the 2x125bp protocol on an Illumina HiSeq 2500 instrument. 6 samples were selected for RNA-Sequencing from each infection (3 from the early time point and 3 from the late time point), along with 3 uninfected control samples. The early stage is when the first malaria symptoms were observed. The late stage is defined as the models peak severity (humane endpoint). These mouse models were then compared to a number of publically available human malaria, both RNA-Seq and microarray, datasets to identify the mouse model(s) that best resembles different human manifestations of this disease at the transcriptomic level (comparative transcriptomics). The insert size has been set to 0 for all paired end sample fastq files because these are unknown. The read length is 125bp.