Ontology highlight
ABSTRACT:
PROVIDER: PRJNA597368 | ENA |
REPOSITORIES: ENA
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Project description:Background: Genetic and epigenetic variability contributes to the susceptibility and pathogenesis of autoimmune diseases. T cells play an important role in several autoimmune conditions, including lupus, which is more common and more severe in people of African descent. To investigate inherent epigenetic differences in T cells between ethnicities, we characterized genome-wide DNA methylation patterns in naïve CD4+ T cells in healthy African-Americans and European-Americans, and then confirmed our findings in lupus patients. Results: Impressive ethnicity-specific clustering of DNA methylation profiling in naïve CD4+ T cells was revealed. Hypomethylated loci in healthy African-Americans were significantly enriched in pro-apoptotic and pro-inflammatory genes. We also found hypomethylated genes in African-Americans to be disproportionately related to autoimmune diseases including lupus. We then confirmed that these genes, such as IL32, CD226, CDKN1A, and PTPRN2 were simi‑ larly hypomethylated in lupus patients of African-American compared to European-American descent. Using patch DNA methylation and luciferase reporter constructs, we showed that methylation of the IL32 promoter region reduces gene expression in vitro. Importantly, bisulfite DNA sequencing demonstrated that cis-acting genetic variants within and directly disrupting CpG sites account for some ethnicity-specific variability in DNA methylation.
2016-10-01 | GSE79237 | GEO
Project description:Transcription profiling of permethrin resistant field mosquito samples of Anopheles funestus from three Southern African populations (Mozambique, Malawi and Zambia) compared to a susceptible lab strain FANG
2014-10-01 | E-MTAB-2216 | biostudies-arrayexpress
Project description:Large DNA viruses are known to manipulate and modify host miRNAs during infection. Therefore the aim of this study was to investigate the impact of infection with the large DNA virus; African swine fever virus (ASFV) on host miRNAs. Small RNA sequencing libraries were prepared from RNA extracted from ASFV (Benin 97/1) infected primary porcine macrophages at 0, 6 and 16 hours post infection. Libraries were pooled and sequenced on 1 lane of an Illumina HiSeq, yielding sequences aligning to a total of 247 different mature Sus scrofa miRNAs. On average, 3779095 (± 1911525) miRNA reads were obtained per sample. The results revealed no widespread modification to host miRNAs, though a number of specific miRNAs were differentially expressed during ASFV infection. Notably, a small number of miRNAs (Ssc-miR-10b, Ssc-miR-144 and Ssc-miR-486) were rapidly upregulated 2-6 fold within the first hour of infection.
2020-07-28 | GSE115512 | GEO
Project description:Epigenetic information can be inherited through the mammalian germline, and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for genes in mice that responded to paternal diet. As part of this analysis, we chracterise the changes in sperm cytosine methylation in response to different diets. Characterizing the RNA exression changes in livers of offspring mice in response to the paternal diet, comparing between low-protein diet and control-diet. Examination the effect of 3 different paternal diets, control diet, Caloric Restriction and low-protein diet, on sperm cytosine methylation.
2011-01-14 | E-GEOD-25898 | biostudies-arrayexpress
Project description:We introduce high-throughput and massive paired-end mapping (PEM), a large-scale genome sequencing method to identify SVs 3 kb or larger that combines the rescue and capture of paired-ends of 3 kb fragments, massive 454 Sequencing, and a computational approach to map DNA reads onto a reference genome. PEM was used to map SVs in an African and putatively European individual and identified shared and divergent SVs relative to the reference genome. Overall, we fine-mapped more than 1000 SVs and documented that the number of SVs among humans is much larger than initially hypothesized; many of the SVs potentially affect gene function. The breakpoint junction sequences of more than 200 SVs were deduced with a novel pooling strategy and computational analysis. Array-CGH was used for validation. Keywords: array CGH
2007-09-28 | GSE9002 | GEO
Project description:Mitochondrial heteroplasmy, the presence of more than one mtDNA variant in a cell or individual is not as uncommon as previously thought. It is mostly due to the high mutation rate of the mtDNA and limited repair mechanisms present in the mitochondrion. The phenomenon has been studied mostly in human samples and in medical contexts. Heteroplasmy has also been researched in other species in fields such as forensics or genetic foot printing, but these studies usually focused on contained families within closely related species. Here we describe a large cross-species evaluation of heteroplasmy in mammals. We employed a novel approach to detect mitochondrial heteroplasmy in both novel and previously reported ChIP-sequencing datasets, which include concomitant mitochondrial DNA sequenced in the experiment. Here, we report novel ChIP-seq experiments for H3K4me1 and CEBPA across mammals, as well as some H3K4me3, H3K27ac and total histone H3 experiments. Most of the reported CEBPA experiments are good quality pull-downs, however the quality of many of the other experiments reported here has not been interrogated in detail. Whereas this does not affect the investigation of mitochondrial DNA pollution for the purposes of this study, both H3K4me1 and total histone H3 ChIP-seq datasets were often sequenced to relatively low depth and showed low ChIP enrichment compared to the other antibodies.
2016-05-13 | E-MTAB-3933 | biostudies-arrayexpress
Project description:The objective of our study is to characterize gene expression signatures associated with in vivo artemisinin-resistance phenotype in this large-scale genome-wide association study. To achieve this goal, we employed microarray technology to establish the global gene expression profiles of isolates sampled from 1043 patients, of whom after treatment with ACTs (artemisinin combination therapy) displayed differential rates of parasite clearance. P. falciparum isolates were sampled from the whole blood of 1043 malaria-infected patients prior to ACT treatment. Sampling was done across 14 field sites spanning across South East Asia (Pailin, Pursat, Preah Vihear, Rattanakiri in Cambodia; Mae Sot, Srisakhet, Khun Han, Ranong in Thailand; Shwe Kyin in Myanmar; Binh Phuoc in Vietnam; Attapeu in Laos), to Bangladesh and African DR Congo from 2010 to 2012. RNA were extracted and synthesis and amplification of target DNA was carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211 (PMID 22990779), to generate sufficient material for hybridizations against a common RNA reference pool of 3D7 strain using a microarray platform.
2014-07-15 | E-GEOD-59097 | biostudies-arrayexpress