Project description:Transcription profiling by array of human skeletal muscle from patients with type 2 diabetes, their first degree relatives and healthy unrelated controls
Project description:Transcription profiling by array of human PBMCs from primary antiphospholipid syndrome and systemic lupus erythematosus patients and healthy controls
Project description:Multiple common variants for celiac disease influencing immune gene expression The goal of this study was to study the effect of genetic variation on gene expression of untouched primary leucocytes. We obtained peripheral blood RNA from unrelated Dutch individuals using PAXgene tubes. We performed a second-generation genome wide association study of 4,533 celiac disease cases and 10,750 controls. We genotyped 113 selected SNPs with PGWAS<10-4, and 18 SNPs from 14 known loci, in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome wide significance (Pcombined<5x10-8), most contain immune function genes (BACH2, CCR4, CD80, CIITA/SOCS1/CLEC16A, ICOSLG, ZMIZ1) with ETS1, RUNX3, THEMIS and TNFRSF14 playing key roles in thymic T cell selection. A further 13 regions had suggestive association evidence. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P<0.0028, FDR 5%) with cis gene expression. *** Due to privacy concerns, the SNP data is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access directly from the submitter (contact info below). ***
Project description:Multiple common variants for celiac disease influencing immune gene expression The goal of this study was to study the effect of genetic variation on gene expression of untouched primary leucocytes. We obtained peripheral blood RNA from unrelated Dutch and UK individuals using PAXgene tubes. We performed a second-generation genome wide association study of 4,533 celiac disease cases and 10,750 controls. We genotyped 113 selected SNPs with PGWAS<10-4, and 18 SNPs from 14 known loci, in a further 4,918 cases and 5,684 controls. Variants from 13 new regions reached genome wide significance (Pcombined<5x10-8), most contain immune function genes (BACH2, CCR4, CD80, CIITA/SOCS1/CLEC16A, ICOSLG, ZMIZ1) with ETS1, RUNX3, THEMIS and TNFRSF14 playing key roles in thymic T cell selection. A further 13 regions had suggestive association evidence. In an expression quantitative trait meta-analysis of 1,469 whole blood samples, 20 of 38 (52.6%) tested loci had celiac risk variants correlated (P<0.0028, FDR 5%) with cis gene expression. *** Due to privacy concerns, the SNP data is not available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access directly from the submitter (contact info below). ***
Project description:Aim: To compare the overall transcriptional profile in healthy controls and celiac disease patients. This dataset, was used to evaluate if our in vitro model (intestinal intraepithelial lymphocytes, desccribed in doi:10.1016/j.jaut.2020.10242 ) is representative of the transcriptional profile in the intestine under healthy or inflammatory conditions. Samples: Upper colonoscopy biopsies from 5 control and 11 celiac disease patients were taken, total RNA was extracted and RNA-sequencing was performed (without replicates)
Project description:RNA sequencing of purified intestinal epithelial cells from paediatric biopsies including Inflammatory Bowel Disease and healthy controls
Project description:Transcriptional profiling of primary human alveolar macrophages challenged with Streptococcus pneumoniae from patients with chronic obstructive pulmonary disease compared to healthy donors