GEO series

Regulation of temozolomide resistance by m6A mRNA methylation in glioma cell lines

GSE306559 Homo sapiens (human) DNA methylation 24 samples Submitted 2026/06/01 Platform GPL34284

At a glance

DNA methylation · human · 24 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Topic: GlioblastomaThis series is part of our curated briefing on it.
Samples: 24 samples: 8 conditions, mostly in triplicateGroups 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)

N6-methyladenosine (m6A) is a critical regulator of mRNA processing and function, playing roles in mRNA processing, translation, and decay. Changes in m6A status have been implicated in various cancers, including glioblastoma (GBM), where acquired chemoresistance to temozolomide (TMZ) remains a major clinical challenge. We developed cell culture models of acquired TMZ resistance in GBM and analyzed the regulation of resistance-associated genes and pathways by m6A.

Read the full summary ↓

We find that key resistance-associated genes and pathways are regulated by m6A methylation, including MGMT, the enzyme that repairs primary TMZ-induced DNA damage. Inhibition of METTL3 with STM2457 treatment destabilizes MGMT mRNA. Intriguingly, other TMZ resistance-associated genes are similarly regulated by m6A, suggesting that METTL3 inhibition may represent a promising therapeutic approach for overcoming TMZ resistance.

This dataset

Open GSE306559 in finder → Find more human RNA-seq datasets → Glioblastoma landscape →

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 GSE306559_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 PRJNA1311120 and SRA study SRP612773. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 conditions, mostly in triplicate

U87 MG, DMSO, ×3 U87 MG, STM2457, ×3 U87-R, DMSO, ×3 U87-R, STM2457, ×3 LN229, DMSO, ×3 LN229, STM2457, ×3 LN229-R, DMSO, ×3 LN229-R, STM2457, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 of them. 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

GSM9203342 U87 MG, DMSO, rep 1 U87 MG, DMSO,
GSM9203343 U87 MG, DMSO, rep 2 U87 MG, DMSO,
GSM9203344 U87 MG, DMSO, rep 3 U87 MG, DMSO,
GSM9203345 U87 MG, STM2457, rep 1 U87 MG, STM2457,
GSM9203346 U87 MG, STM2457, rep 2 U87 MG, STM2457,
GSM9203347 U87 MG, STM2457, rep 3 U87 MG, STM2457,
GSM9203348 U87-R, DMSO, rep 1 U87-R, DMSO,
GSM9203349 U87-R, DMSO, rep 2 U87-R, DMSO,
GSM9203350 U87-R, DMSO, rep 3 U87-R, DMSO,
GSM9203351 U87-R, STM2457, rep 1 U87-R, STM2457,
GSM9203352 U87-R, STM2457, rep 2 U87-R, STM2457,
GSM9203353 U87-R, STM2457, rep 3 U87-R, STM2457,
GSM9203354 LN229, DMSO, rep 1 LN229, DMSO,
GSM9203355 LN229, DMSO, rep 2 LN229, DMSO,
GSM9203356 LN229, DMSO, rep 3 LN229, DMSO,
GSM9203357 LN229, STM2457, rep 1 LN229, STM2457,
GSM9203358 LN229, STM2457, rep 2 LN229, STM2457,
GSM9203359 LN229, STM2457, rep 3 LN229, STM2457,
GSM9203360 LN229-R, DMSO, rep 1 LN229-R, DMSO,
GSM9203361 LN229-R, DMSO, rep 2 LN229-R, DMSO,
GSM9203362 LN229-R, DMSO, rep 3 LN229-R, DMSO,
GSM9203363 LN229-R, STM2457, rep 1 LN229-R, STM2457,
GSM9203364 LN229-R, STM2457, rep 2 LN229-R, STM2457,
GSM9203365 LN229-R, STM2457, rep 3 LN229-R, STM2457,

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