← BioTransfer GEO Dataset Finder
GEO series

GLIOBLASTOMAS ARE CHARACTERIZED BY A REDUCED NUMBER OF M6A SITES IN LNCRNAs

GSE282642 Homo sapiens (human) RNA-seq (gene expression) 26 samples Submitted 2025/05/20 Platform GPL24106
At a glance

RNA-seq (gene expression) · human · 26 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
GlioblastomaThis series is part of our curated briefing on it.
Samples
26 samples: 17 × GB_LT_Patient vs 9 × LGG_LT_PatientGroups 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.
Paper
m6A-lncRNA landscape highlights reduced levels of m6A modification in glioblastoma as compared to low-grade gliomaMolecular medicine (Cambridge, Mass.) · 2025
Summary (written by the submitters)
Recent studies have suggested the potential role of posttranscriptional N6-methyladenosine (m6A) RNA modifications in diverse biological processes, including tumor development. In contrast to intensively studied mRNA modifications, insufficient information is known so far about the epitranscriptome of long non-coding RNAs (lncRNAs). Furthermore, an epitranscriptome of LncRNAs in glioma pathogenesis has not been previously presented.
Read the full summary ↓
Thus, this study aimed to profile m6A modifications within lncRNAs in different grades of gliomas using direct RNA long-read sequencing, with the goal of yielding both nucleotide and transcript-resolved m6A hits as biomarkers for tumor progression. Here we explored ONT direct RNA-seq to detect N6-methyladenosine (m6A) sites within lncRNAs' RRACH motifs in 26 glioma tumor tissues. Generally, 98.5% of m6A-modified RRACH motifs were detected in mRNA transcripts, and 1.16% in lncRNAs. We identified 60-748 unique m6A-modified lncRNAs for individual gliomas. On average, 15.84% of all RRACH motifs within lncRNAs were modified in glioblastomas (GB), while the m6A frequency reached 23.73% in the low-grade glioma (LGG) group. Unsupervised clustering analysis based on lncRNAs' m6A status resulted in three m6A clusters. Patients within the highly modified lncRNAs cluster (C3) experienced significantly longer survival compared to patients with lower methylation rates who were clustered into C1/C2 (2901 days in C3 vs 439 days in C1, log-rank test p=0.019).  In summary, we discovered that lncRNAs are highly modified in LGG while multiple epi-marks, found in low-grade gliomas, are absent in GB tissues revealing m6A contribution to glioma pathology.
Published in
m6A-lncRNA landscape highlights reduced levels of m6A modification in glioblastoma as compared to low-grade glioma
Steponaitis G, Dragunaite R, Stakaitis R et al. · Molecular medicine (Cambridge, Mass.) 2025 · PMID 40382536 · doi:10.1186/s10020-025-01254-x
This dataset
Open GSE282642 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 GSE282642_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1189527 and SRA study SRP547032. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40382536) ↗
Study design
17 × GB_LT_Patient vs 9 × LGG_LT_Patient

Supports a between-group comparison across 26 samples.

How we read this: 2 replicated groups read from 26 sample titles; they account for 26 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
More Glioblastoma datasets

Search all human RNA-seq datasets in GEO →

Share this dataset

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.