CBA × C57BL/6 F1 (CBF1) mice were infected with 400 L3 infective-stage H. bakeri larvae by gavage and adult nematodes were collected from the small intestine 14 days post infection. The nematodes were washed and maintained in serum-free medium in vitro as described previously (17 ). For genomic analyses, DNA was collected from adult worms immediately following harvest from the gut, with extensive washing to remove host material followed by purification using Zymo Research Genomic DNA Clean & Concentrator kit following manufacturer’s instructions (further details in Supplementary Methods). RNA from H. bakeri was collected from adult worms in Qiazol (Qiagen) using mechanical disruption with 5 mm stainless steel beads (Qiagen) on a Tissue Lyser II (Qiagen). Caenorhabditis elegans were harvested and flash frozen as in (18 (link)). Total RNA was treated with RNA 5′ Polyphosphatase (Epicenter) following manufacturer’s instructions, before library preparation. Libraries for small RNA sequencing were prepared using the CleanTag small RNA library prep kit (Trilink) according to manufacturer’s instructions.
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