Rodriguez Valle et al 2017 Transcriptome and toxin family analysis of the paralysis tick, Ixodes holocyclus, Supplementary Table 2

Top 1000 differentially expressed genes between salivary gland and viscera transcriptome datasets. High quality Illumina reads sequenced for salivary gland (SG3 and SG5) and viscera (VIS4 and VIS6) samples were aligned onto 68,066 Ixodes holocyclus reference transcripts using Bowtie 2 (Langmead and Salzberg, 2012). Aligned raw counts were calculated using SAMtools (Li et al., 2009) and differential expressed transcripts between Salivary Gland and Viscera samples was calculated using edgeR (Robinson et al., 2010) with genes with at least a read per million in three samples. The tool eXpress (Roberts and Pachter, 2013) was used to calculate gene expression statistics including normalised read counts and fragments per kilobase of exon per million mapped reads (FPKM). Annotation of I. holocyclus transcripts was performed using AutoFACT (Koski et al., 2005).