Datasets and code - transcriptomic response African fruit bats to immune challenge

Results and underlying R code from differential expression analysis used to investigate the transcriptomic response of African fruit bats to immune challenge with recombinant vaccines expressing Ebola or Nipah virus antigens.The datasets contain detailed information on all differentially expressed genes in Eidolon helvum after exposure to a Nipah or Ebola vaccine. Dataset S1 contains genes differentially expressed between a control (PBS) individual and a group of bats exposed to a Nipah vaccine. Dataset S2 contains genes differentially expressed between a control (PBS) individual and a group of bats exposed to an Ebola vaccine. Dataset S3 contains genes differentially expressed between the Ebola vaccine and Nipah vaccine exposed bats.As described in more detail in Jax et al. 2025, E. helvum bats were split into three groups to receive one of three treatments: Ebola vaccine, Nipah vaccine or saline injections. The first group received an intramuscular dose of recombinant chimpanzee adenovirus vaccine (ChAdOx1) encoding the Ebola Guinea virus glycoprotein, followed four weeks later by an intramuscular dose of Modified Vaccinia Ankara vaccine (MVA) encoding the same Ebola virus G protein. The second group received an intramuscular dose of recombinant chimpanzee adenovirus vaccine (ChAdOx1) encoding the Nipah virus G protein, followed four weeks later by an intramuscular dose of Modified Vaccinia Ankara vaccine (MVA) with no Nipah virus antigen. The third group received two doses of Phosphate Buffered Saline (PBS) four weeks apart. Blood samples were collected weekly and organs were harvested following euthanasia at the end of the experiment. The RNA extraction and sequencing, read quality check and read mapping is described in more detail in Jax et al. 2025.After excluding samples with low quality RNA following extraction, we carried out sequence analysis using data from one PBS control individual, two or three Nipah vaccine treated bats, and six to eight Ebola vaccine treated bats depending on the time point and tissue type. To investigate which genes were up- or downregulated in response to each vaccine, gene expression levels between the control group and each vaccine group were compared in blood samples at each time point (1w-8w ps) and in each tissue type (kidney, lung, spleen) at eight weeks after first vaccine exposure. No comparison was made between the control group and the vaccine groups two weeks after vaccine exposure, as the RNA from the single included control individual from that time point had poor quality and was therefore not sequenced. In addition, no comparison was made five weeks post vaccine exposure in the Nipah vaccine group as there was only one sample with high quality RNA for that treatment and time point. To identify genes that were differentially expressed in the Nipah and the Ebola vaccine group, gene expression levels were further compared between each vaccine group in blood samples from one to four weeks ps. All differential gene expression analyses were conducted in DESeq2 v 1.36.0, which take the low number of replicates into account. P-values were adjusted using the Benjamini and Hochberg false discovery rate (FDR) correction for multiple testing. Genes with an FDR <0.05 were considered differentially expressed.R code and original data files required for reproducing the main differential expression analyses is also available in this figshare folder.For more details, see Jax et al. 2025 (Serological and transcriptomic response of African fruit bats to immune challenge with recombinant vaccines expressing Ebola or Nipah virus antigens)