Pluto Bioinformatics

GSE102789: RNAseq of duodenal tissue from C57BL/6 mice both susceptible and resistant to Heligmosomoides polygyrus

Bulk RNA sequencing

Purpose: Identify genes implicated in resistance to H. polygyrus; Method: RNA was extracted from duodenal tissue from C57BL/6 mice during primary and secondary H. polygyrus. Total RNA libraries were created using the Encore Complete RNA-Seq Library Systems kit (NuGEN), following manufacturers instructions. Total RNA libraries were sequenced using the Illumina HiSeq 2500. The raw Illumina reads were analysed as follows. First, the data quality was analysed using FastQC. Then the low quality bases were trimmed using Trimmomatic. The read pairs which passed the trimming quality filters were then aligned to mm10 (Ensembl version 75) using Tophat2. Counts were determined using htseq_count. Normalisation and statistical analysis was performed using edgeR. Differential gene analysis was calculated from nave control group (A). Statistically significant genes with FDR < 0.05 are reported.; Results: Following analysis, we identified many transcripts significantly different from the nave control following primary and secondary H. polygyrus infection.; Conclusions: The intestinal transcriptome of both primary and secondary infected mice differ significantly, identifying qualitative and quantitative differences between susceptible (primary infected) and resistant (secondary infected) mice. SOURCE: Lewis,James,Entwistle (lewis.entwistle@crick.ac.uk) - Allergy and Anti-Helminth Laboratory The Francis Crick Institute