Please find the following data archived from 'Transcriptional responses in a Drosophila defensive symbiosis' by Hamilton et al., Molecular Ecology: 1. All contigs assembled for the reduced (see text) version of the Trinity transcriptome assembly containing Drosophila neotestacea, Howardula aoronymphium and unnamed trypanosomatid(s). 2. Contigs putatively identified as Spiroplasma from the reduced and reduced assemblies. 3. A list of contig IDs putatively identified as Drosophila, Howardula, or trypansomatid. 4. Results of differential expression analysis of transcripts identified as Drosophila and having annotation in FlyBase. Raw read counts are as follow: reads1 = S-HA- treatment reads2 = S-HA+ reads3 = S+HA- reads4 = S+HA+ P-values calculated using DESeq, and normalized read counts (output from DESeq) are also included. 5. rt-QPCR relative expression values for target transcripts. Treatments/infections are coded for 0 as the absence of the treatment and 1 as the presence. 6. Spiroplasma infection intensities used to generate Fig. 1 7. Spiroplasma RIP expression used to generate Fig. 4. Spiroplasma infection intensity (dnaA copies in genomic DNA) is included for 1-day old flies as a normalized absolute count.