GEO series

Genome‑wideBrain DNAMethylationandGeneExpression Patterns Unravel Epigenetic Reprogramming in Mesial Temporal Lobe Epilepsy

GSE272142 Homo sapiens (human) DNA methylation 12 samples Submitted 2025/07/31 Platform GPL16791

At a glance

DNA methylation · human · 12 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 12 samples: 9 distinct titles, 1 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Mesial temporal lobe epilepsy (MTLE) is the most common drug-resistant epilepsy in adults, characterized by hippocampus sclerosis. To date, the etiology of MTLE epileptogenesis and the molecular mechanisms underlying hippocampus sclerosis remain largely unclear. Altered genome-wide DNA methylation patterns and differential gene expression have been reported to be involved in the pathophysiological mechanism of epileptogenesis.

Read the full summary ↓

To discover epigenetic reprogramming patterns associated with MTLE, we used a higher-throughput microarray, Illumina Infinium 850 K BeadChip, and RNA sequence to analyze epigenome-wide DNA methylation and related gene expressions. We also performed an enrichment analysis to find differences between the patients and autopsy controls. Through data analysis we identified 1832 DNA differentially methylated sites, and ten differentially methylated regions in several chromosomes. The differentially methylated genes were found enriched in "synaptic vesicle", "synaptic vesicle exocytosis", "regulation of synaptic plasticity", "Parkinson's disease", and "Oxidative phosphorylation". Correlation analysis of RNA expression and DNA methylation revealed that 16/48 genes’ DNA methylation marks residing in the promoter region, and 32/48 were located within the gene body. These findings assist with a better understanding of the molecular pathogenesis of MTLE and aid in designing effective tailored interventions.

This dataset

Open GSE272142 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE272142_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

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

Also filed as BioProject PRJNA1135199 and SRA study SRP519602. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

9 distinct titles, 1 of them repeated

XY ×4

How we read this: Read from 12 sample titles: 9 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM8394070 TLE1_DG
GSM8394071 TLE3_DG
GSM8394072 TLE5_DG
GSM8394073 TLE6_DG
GSM8394074 TLE7_DG
GSM8394075 TLE8_DG
GSM8394076 XY161222
GSM8394077 XY171205
GSM8394078 XY171229
GSM8394079 XY180413
GSM8394080 XYA0513A
GSM8394081 XYA0516B

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.