biostudies-arrayexpressArchibold MposhiMus musculusSeSAMe R Packagehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14387The study explores the specific impact of early life influenza A/H1N1 infection on epigenetic programming within the bone marrow microenvironment. Using a murine model, we investigated how viral infection, occurring during the early life developmental period, can induce lasting changes in the epigenetic landscape of the bone marrow.biostudies-arrayexpressScaning - Illumina Infinium HD Protocol: DNA methylation was assessed using Illumina Infinium Mouse Methylation BeadChips (Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol. Approximately 125ng of bisulfite converted DNA was amplified, fragmented, purified and hybridized onto the beadchip according to the manufacturer’s instructions. After staining, washing and coating, the beadchips were scanned in the Illumina iScan system.Nucleic Acid Extraction - DNA was extracted from frozen mouse bone marrow samples (5 x 106 cells) using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. DNA was eluted in 50µl of water. DNA concentrations, quality and purity of each sample were measured using the Nanodrop and Qubit (Thermo Scientific, Waltham, MA, USA). 500ng of DNA was bisulfite converted using the EZ DNA Methylation™ Kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s instructions.Sample Collection - Bone marrow tissue was harvested and frozen in FCS + 10% DMSO first at -80°C before being 123 stored in liquid nitrogenLabeling - Illumina Infinium HD Protocol: DNA methylation was assessed using Illumina Infinium Mouse Methylation BeadChips (Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol. Approximately 125ng of bisulfite converted DNA was amplified, fragmented, purified and hybridized onto the beadchip according to the manufacturer’s instructions. After staining, washing and coating, the beadchips were scanned in the Illumina iScan system.Hybridization - Illumina Infinium HD Protocol: DNA methylation was assessed using Illumina Infinium Mouse Methylation BeadChips (Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol. Approximately 125ng of bisulfite converted DNA was amplified, fragmented, purified and hybridized onto the beadchip according to the manufacturer’s instructions. After staining, washing and coating, the beadchips were scanned in the Illumina iScan system.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsData Transformation - For preliminary quality control assessment data were exported as idat files and uploaded into GenomeStudio (Illumina). Methylation data were also imported into R Studio (R version 4.3.1) using SeSAMe R package version 1.16.1 and pre-processed. The idat files were read into the R workspace as sigDF objects using the readIDATpair() function with the platform parameter set to “MM285”. Data pre-processing was done using the openSesame() function with the code recommended for mice (“TQCDPBM”) as prep argument, filtering out probes with a detection p > 0.05, using out-of-band probes to correct the signal background, and performing quantile normalization. A β values matrix (filtered_betas_matrix) was created using the getBetas() function, and annotated with the sample metadata and also with the manifest file (mm10 genome build information) (https://zwdzwd.github.io/InfiniumAnnotation#mouse/).MetabolomicsUnknownTranscriptomicsGenomicsProteomicsiScanmethylation profiling by arrayMus musculusArchibold MposhifalseEvidence of epigenetic reprogramming in bone marrow following influenza A (H1N1) infection during early lifeThe study explores the specific impact of early life influenza A/H1N1 infection on epigenetic programming within the bone marrow microenvironment. Using a murine model, we investigated how viral infection, occurring during the early life developmental period, can induce lasting changes in the epigenetic landscape of the bone marrow.2025-12-31T00:00:00Z2025-12-31T02:02:47.915Z2024-08-27T10:16:17.296ZE-MTAB-14387EFO_0002944EFO_0003814EFO_0003813EFO_0002759EFO_0005518EFO_0003816EFO_0003815