GEO series

Epic Methylation analysis on Glycogen Storage Disorder type 1a and Healthy Controls fibroblasts

GSE330325 Homo sapiens (human) DNA methylation 8 samples Submitted 2026/05/12 Platform GPL33022

At a glance

DNA methylation · human · 8 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 8 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

An analysis of differences in the genomic methylation pattern between GSD1a and HC samples using the Illumina EPIC V2 array as shown in the Disease-associated programming of cell memory in glycogen storage disorder type 1a manuscript. To assess the global differences between samples from the two groups, we used the full dataset of processed probes and initially performed a regression analysis with the aim to assess the in-group variability for each of HC and GSD1a groups tested.

Read the full summary ↓

Results from this analysis showed lower variability in the GSD1a group which implies that GSD1a fibroblasts present a methylation phenotype that is consistent between group samples as compared to the HC samples. These differences were also observed by an unsupervised clustering analysis that we performed based on K-means searching for two clusters between our 8 tested samples and by PCA. Differential methylation analysis comparing GSD1a to HC cells was performed. Thousands of significantly different probe signals between the groups were found. Differential methylation region analysis which is based on methylated probes distribution located at similar regions in the genome, obtained many differentially methylated regions (DMR) between the groups. GSEA comparing GSD1a cells to HC cells using the methylation dataset and the GO database revealed significantly enriched pathways related to lysosomal and metabolic pathways. In addition, pathways related to epigenetic modifications are also differentially enriched between GSD1a and HC cells. An integratino of this experiment with ATAC-seq and RNA-seq data is shown in the manuscript.

This dataset

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Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE330325_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1463641. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 8 more — browse all 8 samples with per-sample file links →

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