Fig. 1

Study design. Left-hand panel: To identify genes that are differentially expressed in whole blood samples collected and processed using the PAXgene versus Tempus systems, matching samples of whole blood were collected from 9 healthy individuals (Control 1–9). Samples were processed using either the PAXgene Blood RNA Kit or the Tempus Spin RNA Kit. Gene expression was analyzed by microarray analysis and compared. To examine if differences in sample processing can result in artificial changes in gene expression between healthy and diseased individuals, we compared gene expression in samples from T1D subjects that were obtained from TrialNet (TN-T1D) and the University of Florida (UF-T1D) to that of healthy subjects (Control 1–9). TrialNet samples were collected in Tempus tubes and RNA was isolated using the automated KingFisher Purification system. University of Florida samples were collected in PAXgene tubes and processed using the PAXgene blood RNA kit. Right-hand panel: To examine if sample processing-dependent differences in gene expression are due to degradation of transcripts in the collection tube or loss of transcripts during the RNA extraction procedure, we compared gene expression in matching samples of isolated RNA versus whole blood lysate prepared directly from the collection tubes. For this study, four whole blood samples were collected from 11 healthy individuals (Samples 1–11), and blood lysate and total RNA were prepared from 1 PAXgene tube and 1 Tempus tube each