Microarray analysis of salivary gland CD4+ T cells

Whole human genome arrays were used to assess the transcriptome differences in CD3+CD4+CD45RA- memory T cells isolated and sorted from minor salivary gland biopsy tissue of individuals who met 2002 American European Consensus Group classification criteria for primary Sjogren’s syndrome (SS) and subjects who did not meet criteria for SS, lacked focal lymphocytic sialoadenitis, lacked anti-Ro antibodies, lacked anti-La antibodies, but who had subjective symptoms of dryness (non-SS, sicca controls). Samples from 17 pSS and 15 non-SS subjects were hybridized to Agilent Whole Human Genome 8x60K microarrays in three batches (Batch 1: 2 pSS, 3 non-SS; Batch 2: 6 pSS, 5 non-SS; Batch 3: 9 pSS, 7 non-SS).  All data were pooled to assess potential batch effects by principal components analysis and gene expression data were quality control checked using the arrayQualityMetrics R package. Batch effects were equalized via ComBat analysis (‘Surrogate Variable Analysis’ R package Ver 3.8.0; manual specification of batches).