The CLUSTER consortium (https://www.clusterconsortium.org.uk/) performed RNA sequencing on bulk and sorted CD4, CD8, CD14 and CD19 cells from the peripheral blood of patients with juvenile idiopathic arthritis and healthy controls. These data were used to examine performance of algorithms to impute cell subset specific expression from the mixed cell population (PBMC). Information and processed read counts are provided here for reproducibility purposes. Raw data (FASTQ) and clinical characteristics will be released when the primary outcome paper from the study is published.