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Series GSE60679 Query DataSets for GSE60679
Status Public on Nov 12, 2015
Title A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases (Th17 Treg)
Organism Homo sapiens
Experiment type Expression profiling by array
Summary In this work we present an analytical strategy to systematically identify early regulators by combining gene regulatory networks (GRN) with GWAS. We hypothesized that early regulators in T-cell associated diseases could be found by defining upstream transcription factors (TFs) in T-cell differentiation. Time series expression and DNA methylation profiling of T-cell differentiation identified several upstream TFs, of which TFs involved in Th1/2 differentiation were most enriched for disease associated SNPs identified by GWAS.
Overall design Naïve CD4+ T cells were isolated from buffy coat of four healthy donors using a naïve CD4+ T cell isolation kit (Miltenyi, Bergisch-Gladbach, Germany). Naïve CD4+ T cells were stimulated with TGF-β (1 ng/mL), IL-1β (10 ng/mL), IL-6 (25 ng/mL), IL-21 (25 ng/mL) and IL-23 (25 ng/mL) for Th17, and TGF-β (10 ng/mL) and IL-2 (10 ng/mL) for Treg. Cells were cultured for six days in Iscove’s modified Dulbecco medium (IMDM) supplemented with 2 mM L-glutamine (PAA Laboratories, Linz, Austria), 10% heat-inactivated FCS (PAA Laboratories, Linz, Austria), 5 µM β–mercaptoethanol (Sigma-Aldrich, St. Louis, Missouri, USA) and 50 ug/mL gentamicin (Sigma-Aldrich, St. Louis, Missouri, USA). Cells were cultured for 6 days and then re-stimulated with plate-bound anti-CD3 and soluble anti-CD28 in the presence of corresponding polarizing cytokines and antibodies for another 2 days (Zhang et al. 2013). RNA was extracted using a miRneasy Mini Kit (Qiagen). The RNA concentrations were analysed with NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies). For the gene expression microarray analysis, The cRNA was prepared using a Low Input QuickAmp Labeling Kit. For Th17 and Treg cells the gene expression microarray analysis was performed using SurePrint G3 Human Gene Expression 8x60K v2 microarray kit, according to the manufacture’s instruction (Agilent Technologies).
Contributor(s) Gustafsson M, Gawel DR, Hellberg S, Konstantinell A, Eklund D, Ernerudh J, Lentini A, Liljenström R, Mellergård J, Wang H, Nestor CE, Zhang H, Benson M
Citation(s) 26560356
Submission date Aug 22, 2014
Last update date Jan 09, 2018
Contact name Danuta Gawel
Organization name Linköping University
Street address Garnisonsvägen
City Linköping
ZIP/Postal code 58185
Country Sweden
Platforms (1)
GPL17077 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381 (Probe Name version)
Samples (40)
GSM1484728 S4-Th17-6h
GSM1484729 S4-Th17-24h
GSM1484730 S4-Th17-3d
This SubSeries is part of SuperSeries:
GSE60680 A validated gene regulatory network and GWAS identifies early regulators of T-cell associated diseases
BioProject PRJNA259238

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE60679_RAW.tar 122.2 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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