Data from: DNA methylation in granulocyte-macrophage progenitors differentiated from CD34+ HSPCs
Data files
Jun 22, 2026 version files 823.02 MB
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EPIC_UK-DUE19698.zip
823.01 MB
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README.md
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Abstract
We previously found that transplacental Japanese encephalitis virus (JEV) infection in pregnant pigs is associated with increased IFNα levels in live JEV-exposed fetuses. All control fetuses had no detectable IFNα or levels at the limit of detection in their blood. Our working hypothesis is that during JEV infection in pregnant pigs, surviving fetuses that were exposed in utero to inflammatory cytokines, including IFNα, may carry long-lasting immunopathology at least partially determined by epigenetic alterations. To further test the hypothesis, we employed a reductionist model in which fetal CD34+ hematopoietic stem progenitor cells (HSPCs) obtained from umbilical cord blood were exposed to IFNα during differentiation and used whole-genome methylation to profile epigenetic modifications.
Dataset DOI: 10.5061/dryad.v6wwpzhbq
Description of the data and file structure
This dataset contains the standard output of the methylation microarray with the Infinium MethylationEPIC BeadChip Kit (Illumina) and Illumina iScan: Illumina iScan image files, tables containing sample information, probe signals, control probe profile, and sample methylation profile.
Folders and Files
Folder: EPIC_UK-DUE19698.zip
Description: This dataset contains the standard output of the methylation microarray with the Infinium MethylationEPIC BeadChip Kit (Illumina) and Illumina iScan: Illumina iScan image files, tables containing sample information, probe signals, control probe profile, and sample methylation profile. Specificly:
Subfolder 205058490034:
Contains raw array output files generated by the Illumina iScan instrument.
File Types
- .sdf: Contain sample- and array-specific data generated during image processing and signal extraction by the Illumina iScan system. These files store intermediate information used by Illumina software for probe intensity calculations, quality control, and generation of methylation measurements.
- .text: Contain sample- and array-specific data generated during image processing and signal extraction by the Illumina iScan system, including Registration Score, Mean ON, Mean OFF, Separation Metric Num, ON Signal To Noise Cut Off, Focus Score 1.
- .jpg: Contain sample- and array-specific data generated during image processing and signal extraction by the Illumina iScan system.
- .html: This file contains metadata generated by the Illumina iScan system during image acquisition and processing of the Infinium MethylationEPIC BeadChip. It records scanner settings, image-processing parameters, and quality-control metrics used during signal extraction and methylation analysis.
Subfolder UK-DUE19698:
Stores metadata specific to each read, providing contextual information that aids in the interpretation of the data.
Infinium.assay and UK-DUE19698.bsc – Instrument assay configuration file used during data acquisition. This file contains instrument-specific settings and metadata required by the acquisition software.
Data/ – Analysis directory generated by software containing the project and analysis files listed below:
- UK-DUE19698.project – project file that defines the analysis workspace, including links to the array datasets and analysis settings.
- UK-DUE19698.project.bin – Binary file associated with the project that stores analysis information and project metadata required to open the project correctly.
- UK-DUE19698_DUE19698_DUE19698_nonorm_nobkgd – Contains the array analysis workspace settings used to generate the reported results.
- UK-DUE19698_DUE19698_DUE19698_nonorm_nobkgd.analysis.config (Configuration file) – Stores software configuration parameters associated with the analysis workspace.
- UK-DUE19698_DUE19698_DUE19698_nonorm_nobkgd.analysis (User file) – Stores user-specific display and workspace settings generated by the software.
File 8EPIC_UDE19698_Sample Sheet:
The Excel file contains information about analyzed samples.
Sample_Name
Pat F LT-IFNa
Pat F Control
Pat G LT-IFNa
Pat G Control
Pat H LT-IFNa
Pat H Control
Pat K LT-IFNa
Pat K Control
Pat F-K, indicate CD34+ cells isolated from blood od donors F to K. Control - no interferon treatment. IFNa - cells treated with interferon.
Project ID - UDE19698
Sample_Well – shows the well ID in the plate in which samples were submitted.
File Sample Methylation Profile:
This file contains probe-level DNA methylation measurements generated from the Illumina Infinium MethylationEPIC BeadChip. Each row corresponds to an individual CpG probe, and columns contain methylation and signal intensity measurements for each biological sample analyzed in the study.
File Control Probe Profile:
This file contains quality-control measurements generated from the control probes included on the Illumina Infinium MethylationEPIC BeadChip. Control probes monitor the performance of critical assay steps, including bisulfite conversion, hybridization, extension, staining, target removal, and background signal detection.
File Sample Table:
This file contains sample metadata, array identifiers, chip positions, and summary quality-control metrics generated during processing of the Illumina Infinium MethylationEPIC BeadChip. The table links biological samples to their corresponding array locations and provides signal intensity statistics used for quality assessment. This file serves as the primary sample metadata and quality-control summary table for the methylation array experiment. It links biological samples to array locations and provides signal intensity and probe detection metrics used to evaluate data quality before downstream methylation analyses.
Code/software
Illumina GenomeStudio version 2011.1 (MethylationEPIC v-1-0 B3 annotation file was used).
Human subjects data
CD34+ cells were isolated from human umbilical cord blood. For work with human blood samples, we followed the University of Saskatchewan Human Research Ethics Policy with approval from a Research Ethics Board (16-135). All human participants provided explicit informed consent for publication and public sharing of de-identified data. Prior to analysis and data deposition, all personally identifiable information was removed, including names, dates of birth, geographic identifiers, medical record numbers, and any other direct or indirect identifiers. Samples and datasets were coded using unique study identifiers that could not be linked to participant identities by individuals outside the approved research team. All procedures were conducted in accordance with institutional ethics approval and applicable human subject protection guidelines.
To partially reproduce a fetal environment with excessive IFNα, we treated fetal CD34+ HSPCs with recombinant IFNα or Control media for 24 h. Afterward, for the differentiation assay, IFN-α-treated (for 24 h) CD34+ HSPCs were cultured in a complete methylcellulose medium for 10 days in the presence or absence of IFN-α that resulted in two conditions—IFNα-short-treated (24 h before differentiation) and IFNα-long-treated cells (24 h before differentiation + 10 days during differentiation). For the Control condition, CD34+ HSPCs were not exposed to IFNα at any experimental stage. We analyzed genome-wide DNA methylation in granulocyte-macrophage progenitors differentiated from CD34+ HSPCs in the Control and long-term IFNα treatment conditions. The quantity and quality of genomic DNA were assessed with Qubit and NanoDrop 8000 (Thermo Fisher Scientific). We used 750 ng of DNA for bisulfite conversion with the EpiTect Bisulfite Kit (QIAGEN) and methylation microarray with the Infinium MethylationEPIC BeadChip Kit (Illumina); scanning was done by an Illumina iScan. The Infinium MethylationEPIC BeadChip Kit covers over 850,000 methylation sites quantitatively across the genome at single-nucleotide resolution.