RNA-seq of pooled sample of Mastomys species
We prepared libraries using workflows for the Total Nucleic Acids Library Preparation EF v2.0 and Target Enrichment Standard Hybridization v1.0 Kits (Twist Bioscience). We followed all manufacturers instructions, except for modifications to first strand cDNA synthesis for some samples (more details in Supplementary Material). We diluted experimental samples to a concentration of 3.3 ng/l of background sample and volume of 15l. We performed first strand cDNA synthesis using ProtoScript II (New England Biolabs) for samples with background M1 and M2, while SuperScript II (Thermo Fisher Scientific) was used for samples with background M3 and the negative control. We sequenced pools on an Illumina NextSeq500 using a Mid Output 300-cycle cartridge, 2 x150bp with a target of 16M reads per sample at the MRC-University of Glasgow Centre for Virus Research.