Dataset of methylation data from eosinophil samples isolated from whole blood
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ABSTRACT:
PROVIDER: EGAD00010001594 | EGA |
REPOSITORIES: EGA
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Project description:Genome wide DNA methylation profiles of whole blood from HIV positive men. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 24 subjects from the USA. This data set was used as validation set for studying the effect of HIV viral load on host DNA methylation levels. Bisulphite converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Subjects had different levels of HIV viral load. This dataset reports DNA methylation data set on 24 subjects that were generated in 2012 (while the other data set of 120 subjects reports DNA meth data generated in 2013). Details on what each sample characteristics and their values represent are provided in the 'characteristics_readme.txt' file.
2015-06-09 | E-GEOD-53841 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiles of whole blood from HIV positive men. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 120 subjects from the USA but because of missing clinical characteristics only 109 subjects were used in the scientific publication. The study analyzed the effect of HIV viral load on host DNA methylation levels. Bisulphite converted DNA from the 120 HIV positive men were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Subjects had different levels of HIV viral load. This dataset reports DNA methylation data set on 120 subjects that were generated in 2013 (while the other data set of 24 subjects reports DNA methylation data generated in 2012). Details on what each sample characteristics and their values represent are provided in the 'characteristics_readme.txt' file.
2014-11-03 | E-GEOD-53840 | biostudies-arrayexpress
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| EGAD00010002675 | EGA
Project description:Genome wide DNA methylation profiles of whole blood from HIV positive men. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 24 subjects from the USA. This data set was used as validation set for studying the effect of HIV viral load on host DNA methylation levels.
2015-06-09 | GSE53841 | GEO
Project description:Genome wide DNA methylation profiles of whole blood from HIV positive men. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 120 subjects from the USA but because of missing clinical characteristics only 109 subjects were used in the scientific publication. The study analyzed the effect of HIV viral load on host DNA methylation levels.
2014-11-03 | GSE53840 | GEO
Project description:This data descriptor introduces a curated dataset generated through a methodology that merges differential cell lysis, paired with swift extraction/digestion processes and mass spectrometry-based proteomics, aimed at the specific detection and identification of pathogens such as Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans directly from whole-blood samples. Our protocol offers a rapid and direct diagnostic alternative, circumventing the traditional culture processes and thus facilitating the timely management of diseases like sepsis. We demonstrate the utility of this dataset by proposing a biomarker panel, derived from the proteomic profiles of the aforementioned pathogens, and applying our differential cell lysis protocol to blood samples from 8 sepsis patients. We achieved a sensitivity of 87.5% using parallel reaction monitoring (PRM), thereby providing diagnostics within a seven-hour timeframe without the need for microbial enrichment culture. Moreover, this dataset demonstrates high reproducibility and minimal outliers, solidifying its role as a reference for benchmarking and development of bioinformatic tools for peptide panel in identification for microbial detection, antimicrobial resistance, and epidemiological studies.
2024-08-08 | PXD039165 | Pride
Project description:Cord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells, generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability. We evaluated differences in cell composition and DNA methylation between cord blood buffy coat and whole cord blood samples. Cord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in eight individuals, each contributing buffy coat and whole blood samples. We analyzed principal components (PC) of methylation, performed hierarchical clustering, and computed correlations of mean-centered methylation between pairs. We conducted moderated t-tests on single sites and estimated cell composition. DNA methylation PCs were associated with individual (PPC1 = 1.4 × 10-9; PPC2 = 2.9 × 10-5; PPC3 = 3.8 × 10-5; PPC4 = 4.2 × 10-6; PPC5 = 9.9 × 10-13, PPC6 = 1.3 × 10-11) and not with sample type (PPC1-6>0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired samples ranged from r = 0.66 to r = 0.87. No individual site significantly differed between buffy coat and whole cord blood when adjusting for multiple comparisons (five sites had unadjusted P<10-5). Estimated cell type proportions did not differ by sample type (P = 0.46), and estimated proportions were highly correlated between paired samples (r = 0.99). Differences in methylation and cell composition between buffy coat and whole cord blood are much lower than inter-individual variation, demonstrating that both sample preparation types can be analytically combined and compared.
| S-EPMC5836975 | biostudies-literature