biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsLeslie Zúñiga Macíasmethylation profiling by arrayHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16226This experiment investigates the relationship between maternal fluoride exposure during pregnancy and DNA methylation patterns in the placenta, aiming to identify epigenetic alterations associated with reduced kidney volume at birth. Placental samples were collected from term deliveries and classified according to maternal fluoride concentration and neonatal kidney volume. Genomic DNA was extracted, bisulfite-converted, and hybridized to the Illumina Infinium MethylationEPIC v2.0 BeadChip to quantify methylation across more than 935,000 CpG sites. Data preprocessing, quality control, and normalization were performed using the SeSAMe package in R, following Illumina’s recommended pipeline for EPIC v2.0 arrays. Differentially methylated positions and regions were identified to explore potential epigenetic mechanisms linking prenatal fluoride exposure with altered renal development.biostudies-arrayexpressSample Collection - Placental tissue samples were collected immediately after delivery from healthy term pregnancies. Approximately 3 cm³ fragments were taken from the fetal side of the placenta, rinsed in phosphate-buffered saline (PBS), snap-frozen in liquid nitrogen, and stored at −80°C until DNA extraction.Labeling - 500 ng of genomic DNA were bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA, USA) following the manufacturer’s instructions to ensure complete conversion of unmethylated cytosines.Nucleic Acid Extraction - Genomic DNA was extracted from placental tissue using the QIAamp DNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. DNA purity and concentration were assessed using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and Qubit dsDNA HS Assay Kit (Invitrogen).Hybridization - Bisulfite-converted DNA was hybridized onto the Infinium MethylationEPIC BeadChip v2.0 (Illumina, San Diego, CA, USA) according to Illumina’s standard protocol. Hybridization, washing, and staining steps were performed using the Infinium HD Assay Methylation protocol.Scaning - BeadChips were scanned using the Illumina iScan System to generate raw fluorescence intensity files (.idat). Red and green channel IDAT files were obtained for each sample.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsAdriana Becerra CerveraAlberto Hidalgo BravoLeslie Zúñiga MacíasRafael Velázquez CruzJosé Arreola GuerraFrancisco Avelar GonzálezAlma Guerrero BarreraData Transformation - Raw IDAT files were imported into R (version 4.4.3) and processed using the SeSAMe package. Standard preprocessing steps included detection p-value filtering, background correction, dye-bias equalization, and normalization using the “noob” method implemented in SeSAMe. Quality control was performed to exclude samples or probes not meeting standard QC metrics. Beta values were extracted for all CpG probes for downstream analysis. Differential methylation analysis was conducted using linear models to compare groups based on maternal fluoride exposure and neonatal kidney volume, adjusting for sex and gestational age. CpG sites with adjusted p-value < 0.05 were considered statistically significant.falsePlacental methylation profile in women exposed to fluoride and its association with kidney volume at birthThis experiment investigates the relationship between maternal fluoride exposure during pregnancy and DNA methylation patterns in the placenta, aiming to identify epigenetic alterations associated with reduced kidney volume at birth. Placental samples were collected from term deliveries and classified according to maternal fluoride concentration and neonatal kidney volume. Genomic DNA was extracted, bisulfite-converted, and hybridized to the Illumina Infinium MethylationEPIC v2.0 BeadChip to quantify methylation across more than 935,000 CpG sites. Data preprocessing, quality control, and normalization were performed using the SeSAMe package in R, following Illumina’s recommended pipeline for EPIC v2.0 arrays. Differentially methylated positions and regions were identified to explore potential epigenetic mechanisms linking prenatal fluoride exposure with altered renal development.2026-04-07T00:00:00Z2026-04-07T19:44:00.853Z2025-11-20T13:43:41.481ZE-MTAB-16226EFO_0002944EFO_0003814EFO_0003813EFO_0002759EFO_0005518EFO_0003816EFO_0003815