Gene expression analysis in MZ twins discordant for IAR [in vitro]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Fredrik Barrenas
PROVIDER: E-GEOD-37146 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE37146: Gene expression analysis in MZ twins discordant for IAR [in vitro] GSE37155: Gene expression analysis in MZ twins discordant for IAR [in vivo] Refer to individual Series
2012-04-14 | E-GEOD-37156 | biostudies-arrayexpress
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Project description:Conditional IRF8 KO mice (mice with a conditional allele of Irf8 crossed with CD19-Cre mice) showed increased numbers of both Gene expression data spleen marginal zone (MZ) and Gene expression data spleen follicular (FO) B cells compared to control mice. To evaluate gene expression patterns that distinguished FO or MZ B cells derived from conditional KO and control mice, we used Affymetrix GeneChip® Mouse gene 1.0 ST Array. FACS-sorted MZ and FO B cells from individual mouse were used for RNA extraction and Affyarray hybridization. There were six independent biological replications in each group - six cases of MZ B cells and FO cells in IRF8 conditional KO mice and six cases of MZ B cells and FO cells in control WT mice.
2010-12-20 | E-GEOD-24972 | biostudies-arrayexpress
Project description:The degree to which the level of genetic variation for gene expression is shared across multiple tissues has important implications for research investigating the role of expression on the aetiology of complex human traits and diseases. In the last few years, a number of studies have been published reporting the extent of overlap in expression quantitative trait loci (eQTL) identified in multiple tissues or cell types. Whilst these studies provide important information on the regulatory control of genes across tissues, their limited power means they can typically only explain a small proportion of genetic variation for gene expression. Here, using expression data from monozygotic twins (MZ), we investigate the genetic control of gene expression in lymphoblastoid cell lines (LCL) and whole blood (WB). We estimate the genetic correlation which represents the combined effects of all causal loci across the whole genome and is a measure of the level of common genetic control of gene expression between the two RNA sources. Our results show that, when averaged across the genome, mean levels of genetic correlation for gene expression in LCL and WB samples are close to zero. We support our results with evidence from gene expression in an independent sample of LCL, T-cells and Fibroblasts. In addition, we provide evidence that housekeeping genes, which maintain basic cellular functions, are more likely to have high genetic correlations between the RNA sources than non-housekeeping gene, implying a relationship between the transcript function and the degree to which a gene has tissue specific genetic regulatory control. In this study, the global genetic control of expression levels for 9555 genes were examined from two samples of RNA sources, collected on pairs of monozygotic (MZ) twins. From each individual, gene expression profiles were generated whole blood (WB), collected using the PAXgeneTM tube system, and lymphoblastoid cell lines (LCL). Using expression data collected from MZ twins is a powerful means of estimating the genetic contribution of expression variation. In particular, the observed phenotypic covariance in gene expression in LCLs and WBs between MZ twins can be partitioned into variation due to within-person environmental effects and between-person genetic effects.
2011-10-28 | E-GEOD-33321 | biostudies-arrayexpress
Project description:Gene expression analysis of splenic follicular B cells and marginal zone B cells from B6 and CD19:KLF3 transgenic mice Comparing KLF3-transgenic and non-transgenic follicular B cells by RNA-microarray revealed that KLF3 regulates a subset of genes that was similarly up-/downregulated upon normal MZ B cell differentiation. Indeed, KLF3 expression overcame the lack of MZ B cells caused by different genetic alterations, such as CD19-deficiency or blockade of B-cell activating factor (BAFF)-receptor signaling, indicating that KLF3 may complement alternative NF-κB signaling. Thus, KLF3 is a driving force towards MZ B cell maturation. RNA of splenic follicular B cells and marginal zone B cells were obtained from 4 different mice per group (B6 and CD19:KLF3 mice). 16 samples = 8 individual mice x 2 B cell subsets.
2011-01-29 | E-GEOD-26948 | biostudies-arrayexpress
Project description:We have analyzed miRNA expression profile in FO and MZ B cells to identified differentially expressed miRNAs between this two subsets that could be potencially involved in the regulation of terminal B cell differentiation Spleens from CD19-Creki/+Dicerfl/+ and CD19-Creki/+Dicerfl/fl mice were collected and after erythrocyte lysis, splenocytes were stained with anti-B220, anti-CD21 and anti-CD23 antibodies. B220+CD21brightCD23+ (MZ) and B220+CD21+CD23bright (FO) B cell populations were sorted and total RNA of purified populations was extracted with TRIzol. miRNA microarray hybridations were performed on Mouse miRNA Microarray platform (Agilent Technologies).
2011-11-01 | E-GEOD-25139 | biostudies-arrayexpress
Project description:Monozygotic (MZ) twin pair discordance for childhood-onset Type 1 Diabetes (T1D) is ~50%, implicating roles for genetic and non-genetic factors in the aetiology of this complex autoimmune disease. Although significant progress has been made in elucidating the genetics of T1D in recent years, the non-genetic component has remained poorly defined. We hypothesized that epigenetic variation could underlie some of the non-genetic component of T1D aetiology and, thus, performed an epigenome-wide association study (EWAS) for this disease. We generated genome-wide DNA methylation profiles of purified CD14+ monocytes (an immune effector cell type relevant to T1D pathogenesis) from 15 T1D-discordant MZ twin pairs. This identified 132 different CpG sites at which the direction of the intra-MZ pair DNA methylation difference significantly correlated with the diabetic state, i.e. T1D-associated methylation variable positions (T1D-MVPs). We confirmed these T1D-MVPs display statistically significant intra-MZ pair DNA methylation differences in the expected direction in an independent set of T1D-discordant MZ pairs (P = 0.035). Then, to establish the temporal origins of the T1D-MVPs, we generated two further genome-wide datasets and established that, when compared with controls, T1D-MVPs are enriched in singletons both before (P = 0.001) and at (P = 0.015) disease diagnosis, and also in singletons positive for diabetes-associated autoantibodies but disease-free even after 12 years follow-up (P = 0.0023). Combined, these results suggest that T1D-MVPs arise very early in the etiological process that leads to overt T1D. Our EWAS of T1D represents an important contribution toward understanding the etiological role of epigenetic variation in type 1 diabetes, and it is also the first systematic analysis of the temporal origins of disease-associated epigenetic variation for any human complex disease. Bisulphite converted DNA from the 100 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
2014-04-09 | E-GEOD-56606 | biostudies-arrayexpress
Project description:There is growing evidence that genomic DNA sequence changes occur in individual somatic cells during the lifetime of an individual and accumulation of these changes may influence aging and disease. In light of this, and contradicting reports regarding discordant copy number profiles between MZ twins(BARANZINI et al. 2010; BRUDER et al. 2008), we set out to identify de novo somatic copy number mutations in DNA from blood for MZ twin pairs of Mexican American descent who were participants of the San Antonio Family Heart Study (SAFHS) or San Antonio Family Diabetes/Gallbladder study (SAFDGS). By applying circular binary segmentation (CBS) to B-allele ratio differences we determined that the 3 MZ twin pairs in this study had concordant copy number profiles. We also detected 2 de novo germ-line CNVs in 2 MZ twin pairs from the SAFHS. This study includes data for 4 monozygotic (MZ) twin pairs, and both parents of 2 of these MZ twin pairs. The purpose of this study was to compare concordance of copy number profiles between MZ twins.
2010-12-11 | E-GEOD-25826 | biostudies-arrayexpress
Project description:In this study, we used Illumina Infinium HumanMethylation450 Beadchips to compare DNA methylation profiles in blood from 10 pairs of MZ twins and 8 individuals recruited at 0, 3, 6, and 9 months. MZ Group (Group A) contained 10 pairs of MZ twins ranging from 23 to 74 years old, including 8 female and 12 male subjects.Longitudinal study group (Group B) included a pair of MZ (male) twins and 6 unrelated individuals (3 male, 3 female), aged from 24 to 39. Except subject H, all participants in Longitudinal study group (Group B) were recalled every 3 months for 9 months (0, 3, 6, and 9 m). Subject H was studied only at 0, 6, and 9 months. Bisulphite converted DNA from the 60 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip
2013-10-30 | E-GEOD-51388 | biostudies-arrayexpress
Project description:Objective. Identify novel genes and pathways specific to superficial (SZ), middle (MZ) and deep zones (DZ) of normal articular cartilage. Methods. Articular cartilage was obtained from knees of 4 normal human donors. The cartilage zones were dissected on a microtome. RNA was analyzed on human genome arrays. Data obtained with human tissue were compared to bovine cartilage zone specific DNA arrays. Genes differentially expressed between zones were evaluated using direct annotation for structural or functional features, and by enrichment analysis for integrated pathways or functions. Results. The greatest differences were observed between SZ and DZ in both human and bovine cartilage. The MZ was transitional between the SZ and DZ and thereby shared some of the same pathways as well as structural/functional features of the adjacent zones. Cellular functions and biological processes enriched in the SZ relative to the DZ, include most prominently ECM receptor interactions, cell adhesion molecules, regulation of actin cytoskeleton, ribosome-related functions and signaling aspects such as Interferon gamma, IL4, CDC42Rac and Jak-Stat. Two pathways were enriched in the DZ relative to the SZ, including PPARG and EGFR_SMRTE. Conclusion. These differences in cartilage zonal gene expression identify new markers and pathways that govern the unique differentiation status of chondrocyte subpopulations. 12 samples, 4 donors, 3 conditions each donor (SZ, MZ and DZ), 0 donor replicates, comparisons made between SZ, MZ and DZ to identify differentially expressed genes.
2012-07-31 | E-GEOD-39795 | biostudies-arrayexpress