Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Smoking-associated DNA methylation features link to HIV outcomes [HumanMethylation450 BeadChip]

ABSTRACT: Smoking-associated DNA methylation features link to HIV outcomes [HumanMethylation450 BeadChip]

PROVIDER: PRJNA483456 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Smoking-associated DNA methylation features link to HIV outcomes [HumanMethylation450 BeadChip]

Project description:Smoking is common in people who live with HIV infection and has significant adverse effects on HIV outcomes. The impacts of smoking on methylome has been well established in non-HIV populations. However, the smoking’s effects on host methylome in HIV-positive population has not been investigated and it is unknown if smoking-associated DNA methylation link to HIV outcomes. In this study, we applied machine learning methods selected smoking-associated DNA methylation features to predict HIV related frailty and mortality.

2019-07-23 | GSE117859 | GEO

Smoking-associated DNA methylation features link to HIV outcomes [Infinium MethylationEPIC]

2019-07-23 | GSE117860 | GEO

Smoking-associated DNA methylation features link to HIV outcomes

Project description:Smoking-associated DNA methylation features link to HIV outcomes

| PRJNA483450 | ENA

Smoking-associated DNA methylation features link to HIV outcomes [Infinium MethylationEPIC]

Project description:Smoking-associated DNA methylation features link to HIV outcomes [Infinium MethylationEPIC]

| PRJNA483457 | ENA

Formalin-fixed, paraffin-embedded (FFPE) tissue epigenomics using Infinium HumanMethylation450 BeadChip assays (HM 450K).

Project description:Comparative analysis of reproducibility of Fresh Frozen (FF) derived DNA, FFPE derived DNA and FFPE derived DNA restored using the Infinium FFPE DNA Restoration solution (FFPEr) when used on the Infinium HumanMethylation450 BeadChip assay.

2015-03-25 | GSE66555 | GEO

Methylomic signatures of platinum re-sensitization in ovarian cancer [Illumina HumanMethylation450 BeadChip]

Project description:Epigenetic changes, particularly DNA methylation aberrations have been implicated in acquired resistance to platinum in ovarian cancer. A multi-institutional randomized clinical trial compared a regimen of a DNA methyl transferase (DNMT) inhibitor guadecitabine and carboplatin to physician’s choice chemotherapy for patients with recurrent platinum resistant ovarian cancer. Tumor biopsies or malignant ascites were collected at day 1 of cycle 1 (pre-guadecitabine) and after two cycles of treatment (post-decitabine). The goal of the current study was to analyze guadecitabine-induced DNA methylation and gene expression changes and correlate pretreatment levels with clinical outcomes. Epigenomic and transcriptomic profiling using the Infinium HumanMethylation450 BeadChip (HM450) and RNA sequencing revealed extensive methylation and gene expression changes induced by guadecitabine in ovarian tumors. Ninety-four gene promoters were significantly hypomethylated after treatment with guadecitabine and 949 genes were differentially expressed in pre vs. post-treatment tumors. Pathways associated with immune reactivation and DNA repair were significantly altered by guadecitabine treatment. Expression levels of 1155 genes involved in 25 networks on day 1 of cycle 1 correlated with progression free survival. Increased expression of selected genes (e.g. DOK2, miR193a) silenced through promoter methylation restored platinum sensitivity in ovarian cancer cells. Together, these results support that guadecitabine altered DNA methylation and expression of genes and gene networks correlate with re-sensitization to carboplatin in ovarian cancer patients.

2018-06-05 | GSE102119 | GEO

Critical evaluation of the Illumina MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling [HumanMethylation450]

Project description:We performed a critical evaluation of the new Infinium MethylationEPIC BeadChip microarray. EPIC covers over 850,000 CpG sites, including >90% of the CpGs from the HumanMethylation450 (HM450) BeadChip and an additional 413,743 CpGs. Even though the additional probes improve the coverage of regulatory elements, including 58% of FANTOM5 enhancers, only 7% distal and 27% proximal ENCODE regulatory elements are represented. Detailed comparisons of regulatory elements from EPIC and whole-genome bisulphite sequencing data (WGBS) show that a single EPIC probe is not always informative for those distal regulatory elements showing variable methylation across the region. However, overall data from the EPIC array at single loci are highly reproducible across technical and biological replicates and demonstrate high correlation with HM450 and WGBS data. We show that the HM450 and EPIC arrays distinguish differentially methylated probes, but the absolute agreement depends on the threshold set for each platform.

2016-09-12 | GSE86829 | GEO

In vitro methylation studies in multiple human cell types [HumanMethylation450 array]

Project description:An Infinium microarray (Illumina HumanMethylation450 BeadChip) was used to generate DNA methylation data from human tissue samples.

2022-03-03 | GSE197719 | GEO

A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies

Project description:We developed a comprehensive analysis pipeline to conduct Epigenome-wide Association Studies (EWAS) using the Illumina Infinium HumanMethylation450 BeadChip, based on data from 2,664 individuals, and 36 samples measured in duplicate. We propose new approaches to quality control, data normalisation and batch correction through control-probe adjustment, and demonstrate that these improve data-quality. Using permutation testing we establish a null hypothesis for EWAS, show how it can be affected by correlation between individual methylation markers and present methods to restore statistical independence.

2015-01-22 | GSE55763 | GEO

Genome-wide DNA methylation status of non-B non-C hepatocellular carcinoma assessed by Infinium HumanMethylation450 BeadChip Kit (Illumina, USA)

Project description:Genome-wide DNA methylation analysis for clinical samples from patients in whom non-B non-C hepatocellular carcinoma developed. A pair of tissues (N=43 pairs) from non-tumor background and tumor was provided from every patient. A platform for this experiment was Infinium HumanMethylation450 BeadChip Kit (Illumina, USA).

2017-03-31 | E-MTAB-4169 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data