EPIC INA6
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Patrick Nylund
PROVIDER: E-MTAB-14582 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Multiple myeloma (MM) cell line treated with an inhibitor to EZH2/EZH1 (UNC1999), DNA methylation inhibitor (5-azacytidine), and a combination of both.
2025-12-29 | E-MTAB-14627 | biostudies-arrayexpress
Project description:Here we investigated the molecular response DNMT- and G9a inhibition in multiple myeloma.
2025-12-31 | E-MTAB-13813 | biostudies-arrayexpress
Project description:array-based analysis of genome-wide DNA methylation changes induced by the demethylating drugs 5-azacytidine and CP-4200 on HCT116 cells for 72 hours
2013-06-01 | E-MTAB-702 | biostudies-arrayexpress
Project description:Background: How prenatal smoke exposure affects DNA methylation leading to atopic disorders remains to be addressed. Epigenetic biomarkers informative of prenatal smoke exposure and atopic disorders are wanting. Since most children suffering from atopic dermatitis (AD) continue to develop asthma later in life, we explored whether prenatal smoke exposure e induces DNA methylation and searched for predictive epigenetic biomarkers for smoke related atopic disorders. Methods: Methylation differences associated with smoke exposure were screened by Illumina methylation panel for children from the Taiwan birth panel study cohort initially. Information about development of atopic dermatitis (AD) and risk factors were collected. Cord blood cotinine levels were measured to represent prenatal smoke exposure. CpG loci that demonstrated a statistically significant difference in methylation were validated by methylation-dependent fragment separation (MDFS). Differential methylation in three genes (TSLP, GSTT1, and CYB5R3) was identified through the screen and their functions were investigated. Results: Among these, only thymic stromal lymphopoietin (TSLP) gene displayed significant difference in promoter methylation percentage after being validated by MDFS (p=0.029). TSLP gene was further investigated in a larger sample of 92 children from the cohort. Methylation status of the TSLP 5′-CpG island (CGI) was found to be significantly associated with prenatal smoke exposure (OR=3.59, 95%CI=1.49-8.64; cotinine level 0.10 ng/ml, sensitivity= 77%; specificity = 61%) and with AD (OR=4.77, 95%CI=1.47-15.53). The degree of TSLP 5′CGI methylation inversely correlated with TSLP protein expression levels (per unit: β=－6.69 ng/ml; 95% CIs, －12.80~－0.59; p=0.032). Conclusions: The effect of prenatal tobacco smoke exposure on the risk for AD may be mediated through DNA methylation. Cord blood methylated TSLP 5′CGI may be a potential epigenetic biomarker for environmentally-related atopic disorders. The buffy coat and plasma samples were separated and stored at −80°C. DNA (100 ng-500 ng) was extracted from cord white blood cells. Microarrays have been performed to investigate fourteen samples, which were classified as two groups according to cotinine exposure dosage (7 versus 7 : high exposure verses low exposure).
2013-12-31 | E-GEOD-35222 | biostudies-arrayexpress
Project description:Differential DNA methylation was identified in CdLS, and correlates to cohesin binding as well. However, DNA methylation may only be one of several events that regulate gene expression in humans. 63 Lymphoblastoid cell lines (LCLs) from 39 CdLS probands, 2 RBS probands and 22 gender and racial matched healthy controls were tested on HumanMethylation27 DNA Analysis BeadChip (Illumina) which carries 27,578 highly informative CpG sites derived from the well-annotated NCBI CCDS database
2010-07-07 | E-GEOD-18458 | biostudies-arrayexpress
Project description:array-based analysis of genome-wide DNA methylation changes induced by the demethylating drugs azacytidine and decitabine on HCT116 cells for 24 hours
2010-07-01 | E-MTAB-210 | biostudies-arrayexpress
Project description:Array-based analysis of genome-wide DNA methylation changes induced by the demethylating drugs azacytidine and decitabine on HCT116 and HL60 cells for 24 hours
2010-12-01 | E-MTAB-417 | biostudies-arrayexpress
Project description:array-based analysis of genome-wide DNA methylation changes induced by the demethylating drugs 5-azacytidine and CP-4200 on U937 cells for 72 hours
2013-07-24 | E-MTAB-1529 | biostudies-arrayexpress
Project description:Glycoproteomics is likely to identify Mtb virulence factors because glycoproteins on the bacterial cell envelope are used by mycobacteria to enter the primary human host cell, the macrophage. It has been proposed that Mtb interacts with mannose receptors on host cells via mannosylated proteins to enter the macrophages. Despite the vital importance of these proteins in Mtb pathogenesis, our current knowledge of Mtb glycoproteins is still limited, and only a few secreted and cell wall-associated glycoproteins have to date been described. Previous studies have used laboratory strains as model systems to study glycosylation in Mtb. However, only a few sub-groups within the genetically conserved MTBC appear to cause extensive outbreaks with different clinical presentation and AMR. In this study, we employed qualitative and quantitative mass spectrometry and bioinformatics to explore the glycoproteomic patterns of clinical isolates from four lineages of the MTBC, lineages 3, 4, 5 and 7, to investigate the role of protein glycosylation in Mtb adaptation, survival and AMR.
2019-03-25 | PXD009676 | Pride
Project description:Reactive nitrogen species (RNS) are the major antimicrobial molecules secreted by host cells to tackle Mycobacterium tuberculosis (Mtb) infection. Mtb respond and adapt to adverse environmental stressors by changes in gene expression, ensuring their survival. This adaptation process is mediated by a combination of transcriptional regulatory networks that result in altered gene expression and enzyme (protein) activities. Previous studies emphasized primarily on transcriptomic response of Mtb to different environmental stresses, including RNS. In this study, the proteomic response of Mtb to sublethal doses of RNS stress after 30 minutes, 2 hours, 6 hours and 20 hours was explored. We used liquid chromatography coupled with electrospray ionization mass spectrometry (LC-MS/MS) to elucidate the proteomic response of Mtb to RNS. Quantitative proteomic analysis revealed identification of 2911 proteins and 6460 acylations in Mtb. A total of 581 unique proteins were found to be affected by RNS at different time points. Multiple-sample test revealed 297 differentially regulated proteins across the four time points. Furthermore, multiple-sample test identified 127 differentially acylated sites on 94 proteins. Marked changes in proteomic response was observed at later time points, most of which were compensatory responses involved in SOS response, iron homeostasis, energy metabolism and other stress responses. This study provides an improved understanding of the dynamic proteomic response of Mtb to RNS and identification of key molecular switches, which is the basis of controlling bacterial growth in different environmental setting.
2022-02-15 | PXD016006 | Pride