Tag: MethylationEPIC

Chemicals Dimethyl sulfoxide (DMSO) was purchased from Sigma-Aldrich (St. Louis, MO, USA), and 5-aza-2′-deoxycytidine (5-aza-dc), trichostatin A (TSA), bisphenol A, benzo[a]pyrene (BaP), benzo[c]fluorene (BcF), and beryllium sulfate (BeSO4) were obtained from Wako Pure Chemical Industries, Ltd. (Osaka, Japan). The SCREEN-WELL Cardiotoxicity Library was purchased from Enzo LifeScience Inc. (Supplementary Table…

NEW YORK – Household income below the poverty level and African American racial identity are associated with faster epigenetic aging, according to a new study. “Environmental factors, including psychological stress, alter gene expression and physiological response through changes in the epigenome,” the authors wrote. “DNA methylation may be the mediation mechanism for the…

Error when changing the database for minfi dropLociWithSnps 2 I am currently filtering Illumina MethylationEPIC data with minfi, which has run smoothly so far. To remove polymorphic CpGs and SBEs I use the following code: NormFlt <- dropLociWithSnps(NormFlt, snps=c(“SBE”,”CpG”), snpAnno=”SNPs.147CommonSingle”) And get the following error: Error in getSnpInfo(object, snpAnno =…

minfi support of illumina Infinium methylationEPIC v2.0 1 @lucas-24386 Last seen 2 days ago Italy Hi all. I have tried to process Infinium methylationEPIC v2.0 with minfi v1.44.0 but it did not work, apparently not recognizing the arrays: function “read.metharray.exp” results in “unknown” for the annotation. Is there a way…

conumee with Infinium MethylationEPIC v2.0 0 @lucas-24386 Last seen 10 hours ago Italy Dear all, we are planning to perform methylation profiling of FFPE tumor samples with the Infinium MetlylationEPIC v2.0 chips, and we would like to use the data to do CNV analysis as well. Can conumee be run…

The following is a summary of “Cell-free DNA in maternal blood and artificial intelligence: accurate prenatal detection of fetal congenital heart defects,” published in the January 2023 issue of Obstetrics and Gynecology by Singh, et al. One crucial process for regulating gene expression in the development of the heart is…

image: Epigenetic Age and Lung Cancer Risk in the CLUE II Prospective Cohort Study view more  Credit: 2023 Michaud et al. BUFFALO, NY- February 16, 2023 – A new research paper was published in Aging (listed as “Aging (Albany NY)” by MEDLINE/PubMed and “Aging-US” by Web of Science) Volume 15, Issue…

doi: 10.1038/s41386-023-01537-z. Online ahead of print. Affiliations Expand Affiliations 1 Emory University, Department of Gynecology and Obstetrics, Atlanta, GA, USA. 2 Department of Psychiatry & Behavioral Health, and Institute for Behavioral Medicine Research, The Ohio State University, Columbus, OH, USA. Anthony.King@osumc.edu. 3 Department of Psychiatry, Michigan Medicine, University of Michigan,…

I want to identify the version of MethylationEPIC from the idat file. 1 I have idat files of Infinium MethylationEPIC. I would like to know if the array of this file is Infinium MethylationEPIC v1.0 or Infinium MethylationEPIC v2.0. Is it possible to investigate the version of the MethylationEPIC from…

Weisman, D. & McKeith, I. Dementia with Lewy Bodies. Semin. Neurol. 27, 042–047 (2007). Article  Google Scholar  Foguem, C. & Manckoundia, P. Lewy Body Disease: Clinical and Pathological “Overlap Syndrome” Between Synucleinopathies (Parkinson Disease) and Tauopathies (Alzheimer Disease). Curr. Neurol. Neurosci. Rep. 2018 18:5 18, 1–9 (2018). CAS  Google Scholar …

Illumina Infinium DNA Methylation (5mC) arrays are a popular technology for low-cost, high-throughput, genome-scale measurement of 5mC distribution, especially in cancer and other complex diseases. After the success of its HumanMethylation450 array (450k), Illumina released the MethylationEPIC array (850k) featuring increased coverage of enhancers. Despite the widespread use of 850k,…

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

From idat Illumina Infinium MethylationEPIC to CNV analysis for homo/hetero-zigous deletion 0 Hi, My group works on cancer and we have difficulty on a little part of our last project about malignant pleuric mesothelioma. I’m looking for help in the analysis of .idat from genome-wide DNA methylation profiles obtained via…