Epigenome analysis of CD4 T cells from treated and untreated patients with multiple sclerosis (MS)
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ABSTRACT:
PROVIDER: PRJNA448427 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome wide DNA methylation profiling of CD4 T cells from treated and untreated patients with multiple sclerosis. The Illumina InfiniumEPIC methylation Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs of CD4 T cells from patients with multiple sclerosis.
2018-04-03 | GSE112596 | GEO
Project description:The aim of this study was to identify differentially expressed genes in peripheral blood mononuclear cells from MS patients that were responders or non-responders to the neuroantigen myelin basic protein. Using microarray we measured mRNA-expression levels in freshly isolated peripheral blood mononuclear cells from 17 untreated patients with multiple sclerosis. Based on studies, measuring the responses of blood derived T-cells to myelin basic protein ex vivo, these 17 untreated MS-patients can be divided into two groups: 4 of the untreated multiple sclerosis patients had T-cells that responded to myelin basic protein ex vivo whereas 13 untreated MS patients had T-cells that did not respond to myelin basic protein ex vivo.
2014-11-28 | E-MTAB-2707 | biostudies-arrayexpress
Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the replication data set (n=102) when we compared gene expression in untreated MS patients (n=27) to healthy controls (n=25).
2013-06-17 | GSE41849 | GEO
Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the discovery data set (n=212) when we compared gene expression in untreated MS patients (n=62) to healthy controls (n=41).
2013-06-17 | GSE41848 | GEO
Project description:Background: pregnancy is associated with reduced activity of multiple sclerosis (MS). However, the biological mechanisms underlying this pregnancy-related decrease in disease activity are poorly understood. This data series contains the subset of data used to generate a MS signature comparing female MS specimens before pregnancy with respect to female MS specimens at ninth month pregnancy.
2010-01-10 | GSE17410 | GEO
Project description:Whole transcriptome RNA-seq analysis to measure group-wise RNA expression level of the MERTK gene in 3 healthy controls (known to be homozygous non-risk haplotype at MERTK gene locus) and to compare this to the group-wise RNA expression level of the MERTK gene in 5 Multiple Sclerosis-affected (MS-affected) individuals (known to be homozygous for the MS risk haplotype at the MERTK gene locus).
2016-02-06 | GSE77598 | GEO
Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the replication data set (n=102) when we compared gene expression in untreated MS patients (n=27) to healthy controls (n=25). The following comparisons were made: untreated MS vs Controls (discovery and replication), untreated vs Interferon treated MS (discovery and replication). For each comparison, respective arrays were processed (background corrected and normalized) together, but seperate from other comparisons. The two time points for controls were averaged. For the first comparison, we report differentially expressed genes at an FDR cutoff of 0.1 at any of the three tested time points in MS patients in the discovery data set. For the second comparison, the FDR cutoff was 0.001. The respective genes were validated in the replication data set when they passed a nominal p-value cutoff of 0.05 at any of the three tested time points.
2013-06-17 | E-GEOD-41849 | biostudies-arrayexpress
Project description:Multiple sclerosis is the most common autoimmune disease of the central nervous system. Studying whole blood RNA from a cohort of 195 MS patients and 66 healthy controls, we identified gene expression signatures for interferon treatment and disease status by microarray analysis. Blood was collected at multiple time points (up to 3 for patients, 2 for controls). Patients were either untreated or treated with Interferon. In total, 626 Affymetrix exon arrays were analyzed, split into discovery and replication data sets. This metadata file contains information on all samples processed in the discovery data set (n=212) when we compared gene expression in untreated MS patients (n=62) to healthy controls (n=41). The following comparisons were made: untreated MS vs Controls (discovery and replication), untreated vs Interferon treated MS (discovery and replication). For each comparison, respective arrays were processed (background corrected and normalized) together, but seperate from other comparisons. The two time points for controls were averaged. For the first comparison, we report differentially expressed genes at an FDR cutoff of 0.1 at any of the three tested time points in MS patients in the discovery data set. For the second comparison, the FDR cutoff was 0.001. The respective genes were validated in the replication data set when they passed a nominal p-value cutoff of 0.05 at any of the three tested time points.
2013-06-17 | E-GEOD-41848 | biostudies-arrayexpress
Project description:Whole transcriptome RNA-seq analysis to measure group-wise RNA expression level of the MERTK gene in 3 healthy controls (known to be homozygous non-risk haplotype at MERTK gene locus) and to compare this to the group-wise RNA expression level of the MERTK gene in 5 Multiple Sclerosis-affected (MS-affected) individuals (known to be homozygous for the MS risk haplotype at the MERTK gene locus). We sequenced the whole transcriptome of 3 healthy control samples which were all homozygous for the MS non-risk haplotype at the MERTK gene. We also did the same RNA-seq protocol on 5 MS-affected subjects that were all homozygous for the Risk haplotype at the MERTK gene. All 8 samples were sequenced evenly across 3 lanes of an Illumina HiSeq NGS machine to remove any batch-type effects that could be caused by sequencing e.g. all cases in one lane and all controls in another lane.
2016-02-06 | E-GEOD-77598 | biostudies-arrayexpress
Project description:MicroRNAs are small noncoding RNA molecules that are involved in the control of gene expression. To investigate the role of microRNA in multiple sclerosis (MS), we performed global microarray analyses of mRNA and microRNA in peripheral blood T-cells from relapsing-remitting MS patients and controls. We identified 2,452 regulated genes and 21 regulated microRNA that differed between MS patients and controls. By Kolmogorov-Smirnov test, 20 of 21 regulated microRNA were shown to affect the expression of their target genes, many of which are involved in the immune system. LIGHT (TNFSF14) was a microRNA target gene significantly decreased in MS. The down-regulation of mir-494 and predicted mRNA-target LIGHT was verified by real-time PCR and we could demonstrate decreased serum levels of LIGHT in MS. Thus, regulated microRNA were significantly associated with both gene and protein expression of a molecule in immunological pathways. These findings indicate that microRNA may be important regulatory molecules in T-cells in MS. Microarray expression analysis of mRNA and miRNA in peripheral blood T-cell of control and MS patients
2013-08-02 | E-GEOD-43590 | biostudies-arrayexpress