title: Autoimmune disease-associated gene expression is reduced by BET-inhibition.
abstract: For many autoimmune diseases, the underlying mechanism is still unknown. In order to get more insight into the etiology of autoimmune diseases, we recently published a study were we performed epigenetic profiling and RNA sequencing on CD4(+)CD45RO(+) T cells derived from the site of inflammation of Juvenile Idiopathic Arthritis (JIA) patients and compared this with healthy controls [1]. In this "Data in Brief", we focus on the analysis of our RNA sequencing data reported in this study, of which the raw and processed files can be found in GEO under GSE71595. We provide a detailed description of the downstream analysis, quality controls, and different analysis methods or techniques that validate the results obtained with RNA-sequencing.
authors.affiliation: Dept. of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands.
authors.forename: Janneke G C
authors.initials: JG
authors.lastname: Peeters
authors.affiliation: Dept. of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands.
authors.forename: Stephin J
authors.initials: SJ
authors.lastname: Vervoort
authors.affiliation: Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508 GA, The Netherlands; Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands.
authors.forename: Gerdien
authors.initials: G
authors.lastname: Mijnheer
authors.affiliation: Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508 GA, The Netherlands; Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands.
authors.forename: Sytze
authors.initials: S
authors.lastname: de Roock
authors.affiliation: Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508 GA, The Netherlands; Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands.
authors.forename: Sebastiaan J
authors.initials: SJ
authors.lastname: Vastert
authors.affiliation: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands.
authors.forename: Edward E S
authors.initials: EE
authors.lastname: Nieuwenhuis
authors.affiliation: Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508 GA, The Netherlands; Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands.
authors.forename: Femke
authors.initials: F
authors.lastname: van Wijk
authors.affiliation: Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508 GA, The Netherlands; Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands.
authors.forename: Berent J
authors.initials: BJ
authors.lastname: Prakken
authors.affiliation: Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands.
authors.forename: Michal
authors.initials: M
authors.lastname: Mokry
authors.affiliation: Dept. of Cell Biology, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands; Laboratory of Translational Immunology, University Medical Center Utrecht, Utrecht 3508 GA, The Netherlands; Division of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, The Netherlands.
authors.forename: Jorg
authors.initials: J
authors.lastname: van Loosdregt
keywords: Autoimmune disease; BET-inhibition; Juvenile Idiopathic Arthritis; RNA-sequencing