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.
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.
Project description:Microarray expression profiling approach was used to identify age-related mRNA markers. In this dataset, we include the expression data obtained from whole venous blood samples collected from ERF (Erasmus Rucphen Family study) donors of different age. Two age groups - young (~25 y.o.) and old (~ 60 y.o.) were analyzed using Partek GS software.
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.
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.
Project description:This is a re-analysis of parts of the dataset deposited in PXD028605 (DOI: 10.1021/acs.jproteome.1c00971, PubMed: 35166117) with databases created by ProtGraph. We only changed the data processing, the sample creation and processing is the same as in the original submission. ProtGraph allows to incorporate variant and further feature information, which changes the amino acid composition of consensus/canonical sequences in a database and is commonly not used in the database analysis.
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.