Comprehensive DNA Methylation Analysis

Genomic DNA was extracted in triplicate from early and Sen BMSCs and HUVECs and from BMSC-derived adipocytes and osteoblasts using Qiagen’s QiAmp mini kit following the manufacturer’s recommendations. Next, 1 μg DNA was bisulfite-converted using EZ DNA Methylation (Zymo Research, Irvine, CA, USA) and analyzed by the Infinium Human MethylationEPIC BeadChip (Illumina Inc., San Diego, CA, USA) according to the manufacturer’s instructions. Raw data were extracted using minfi R package [20 (link)] and normalized using the preprocessFunnorm function. Not-reliable probes according to Zhou and collaborators [21 (link)] and probes on X and Y chromosomes were removed. The remaining 748,241 probes were annotated according to IlluminaHumanMethylationEPICanno.ilm10b4.hg19 annotation data.

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Giuliani A., Bacalini M.G., Ramini D., Mensà E., Giordani C., Xumerle L., Garagnani P., Olivieri F., Procopio A.D., Rippo M.R, & Sabbatinelli J. (2023). Genome-Wide Methylation Changes Associated with Replicative Senescence and Differentiation in Endothelial and Bone Marrow Mesenchymal Stromal Cells. Cells, 12(2), 285.

Publication 2023

QiAmp mini kit Infinium Human MethylationEPIC BeadChip

Adipocytes Bisulfite Dna methylation Genomic Human Osteoblasts Y chromosomes

Corresponding Organization : Marche Polytechnic University

Other organizations : Istituto delle Scienze Neurologiche di Bologna, Istituti di Ricovero e Cura a Carattere Scientifico, Istituto Nazionale di Riposo e Cura per Anziani, Center for Genomic Science, University of Bologna, Karolinska University Hospital, Karolinska Institutet, Policlinico S.Orsola-Malpighi, Istituto di Genetica Molecolare

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Variable analysis

independent variables

Early and Sen BMSCs
HUVECs
BMSC-derived adipocytes
BMSC-derived osteoblasts

dependent variables

DNA methylation profiles

control variables

Genomic DNA was extracted in triplicate
1 μg DNA was bisulfite-converted
Probes on X and Y chromosomes were removed
Not-reliable probes according to Zhou and collaborators were removed

controls

No positive or negative controls were explicitly mentioned in the input protocol.

Annotations

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