Whole blood RNA-Sequencing from children with bacterial infection, viral infection, Kawasaki disease, MIS-C and healthy controls,

RNA-Sequencing was performed on whole blood from 50 children with: confident viral infection (3), MIS-C (21) and healthy controls (10) as well as one adult healthy control. Samples were taken across timepoints 1-3 (acute illness, post-treatment and convalescence). Blood was stimulated for 16-24hrs using QuantiFERON collection tubes(Qiagen) and subsequently stored in a PAXgene blood RNA tube. In addition to unstimulated blood stimulation was performed for CD4+ specific SARS-CoV-2 receptor binding domain peptides, CD4+/CD8+ specific SARS-CoV-2 peptides or mitogen. Total RNA was extracted using PAXgene Blood miRNA kit (Qiagen) followed by additional DNAse treatment using RNA clean & concentrator kit (Zymo Research). Paired-end unstranded RNA-Sequencing was performed on a NovaSeq PE150 platform (Novogene Ltd., UK). Gene level read counts were generated using STAR alignment to the human genome (ensembl GRCh38 version 109).