The parasitic fluke Schistosoma mansoni dwells within the mammalian host blood vessels, in constant risk of being damaged by host immune responses or lost during the migration. The molecular mechanisms that allow the survival of the parasites within its host are yet to be fully understood, particularly during the early stages of infection where it would be a lucrative point of intervention. In order to gain further insight into host-parasite interactions during the intra-mammalian developmental stages, we generated RNA-seq-based transcriptome of S. mansoni collected from experimentally infected mice at days 6, 13, 17, 21, 28, and 35 post-infection. This is the first comprehensive ex vivo intra-mammalian time-course transcriptome study that, for the first time, included a snapshot of the parasite transcriptome during lung stage. The outputs of this work provide a large data resource for the research community and propose avenues for further characterisation of host-parasite interaction mechanisms that would lead to the discovery of novel control strategies for this neglected tropical disease pathogen. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
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