biostudies-arrayexpressAgustín FernándezHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-7719Nanomaterials have lots of promising applications, and concern has risen about their impact to human health. Here, we have analyzed the genome-wide DNA methylation changes associated to the exposure to reduced graphene oxide (rGO) in human lung epithelial cells. Six conditions were assayed, with two technical replicates per condition (12 arrays in total): control, 1 and 10 µg/mL of rGO for 15 or 30 days of exposure.biostudies-arrayexpressLabeling - Labelling was performed automatically during the post-amplification xStain process and is achieved using Biotin and DNP labelled antibodies.Growth Protocol - Human airway epithelial cells BEAS-2B cells were cultured as a monolayer with serum-free BEGM medium (Bronchial epithelial cell growth medium, Lonza, Walkersville, Maryland, USA) in culture dishes. This medium is complemented with the following factors: retinoic acid, insulin, hydrocortisone, transferrin, epinephrine, triiodothyronine, Bovine Pituitary Extract, hEGF (human epidermal growth factor) and GA-1000 (Gentamicin and Amphotericin). Cultures were maintained at 37ºC in a humified atmosphere of 5% CO2.Sample Collection - BEAS-2B cells were cultured with 0, 1 or 10 ug/mL reduced rGO for 15 or 30 days, subsequently pellets were collected.Scaning - IDAT files were processed using the R/Bioconductor package minfi (version 1.22.1) and differentially methylated probes were extracted with the R/Bioconductor package limma (version 3.32.10)Nucleic Acid Extraction - Genomic DNA was extracted with the phenol-chloroform procedure and quantified with the Nanodrop-2000C Spectrophotometer.Hybridization - The arrays were scanned with iScan (Illumina) in accordance with the manufacturer's protocol.Sample Treatment - The rGO stock solution was prepared following the Nanogenotox 2011 protocol (2011 X Nanogenotox - Jensen KA). In brief, 81.5 µL 100% of ethanol were added onto 40 mg of rGO material by slow dripping into a rotating tube tilted 45º. Afterwards, 16.3 mL of a 0.05% BSA (bovine serum albumin) aqueous solution were added to a final rGO concentration of 2.44 mg/mL. This solution was subsequently dispersed by sonication in an ice-cold bath at 40 Hz for 20 minutes with shaking every 5 minutes. Once prepared, the stock solution was stored at 4ºC.For rGO exposure, the working dilutions of 1 and 10 µg/mL were prepared directly in cell culture medium. 150 cm2 dishes were seeded with 106 cells, which were left to attach for 4-8 hours prior to the addition of the nanomaterials. Exposition medium was renewed every 4-5 days, subculturing at 90% confluence.MIAME ScoreRaw DataOrganizationAssays and DataProcessed DataMAGE-TAB FilesArray DesignsData Transformation - Background correction was applied with the NOOB method. Probe signals were further corrected using the BMIQ algorithm. Sex chromosome, SNP-overlapping and multi-mapping probes were filtered out.UnknownTranscriptomicsGenomicsProteomicsThe presence of nanomaterials in our everyday life is ever increasing, and so too are concerns about the possible health consequences of exposure to them. While evidence of their biological activity is growing, there is still scant knowledge of the epigenetic mechanisms that could be at play in these processes. Moreover, the great variability in the chemical and physical structures of these compounds handicaps the study of their possible health risks. Here we have synthesized reduced graphene oxide (rGO) through the thermal exfoliation/reduction of graphite oxide, and characterized the resulting material. We have then made use of Illumina's MethylationEPIC arrays and bisulphite pyrosequencing to analyse the genome-wide and global DNA methylation dynamics associated with the medium-term exposure of human lung epithelial cells to rGO at concentrations of 1 and 10 µg/mL. The results show no genome-wide or global DNA methylation changes associated with either condition. Our observations thus suggest that medium-term rGO exposure does not have significant effects on the DNA methylation patterns of human lung epithelial cells.methylation profiling by arrayHomo sapiensNo genome-wide DNA methylation changes found associated with medium-term reduced graphene oxide exposure in human lung epithelial cellsRaul F. Perez, Anna Yunuen Soto Fernandez, Pablo Bousquets Muñoz, Marta I. Sierra, Juan Ramon Tejedor, Paula Morales-Sanchez, Adolfo F. Valdes, Ricardo Santamaria, Clara Blanco, Ramon Torrecillas, Mario F. Fraga & Agustin F. FernandezAgustín FernándezMario FragafalseMethylation arrays (MethylationEPIC) of human lung epithelial BEAS-2B cells exposed to reduced graphene oxideNanomaterials have lots of promising applications, and concern has risen about their impact to human health. Here, we have analyzed the genome-wide DNA methylation changes associated to the exposure to reduced graphene oxide (rGO) in human lung epithelial cells. Six conditions were assayed, with two technical replicates per condition (12 arrays in total): control, 1 and 10 µg/mL of rGO for 15 or 30 days of exposure.2019-09-16T00:00:00Z2022-01-31T19:06:18.595Z2022-01-31T19:06:18.595ZE-MTAB-7719EFO_0002944EFO_0003814EFO_0003813EFO_0003789EFO_0002759EFO_0005518EFO_0003816EFO_0003815EFO_000396910.1080/15592294.2019.1666650