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Epigenetic therapy activates TE-chimeric transcripts to provide additional source of antigens in glioblastoma stem cells

GSE227059 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 112 samples Submitted 2024/06/05 Platform GPL18573Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 112 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Topic
GlioblastomaThis series is part of our curated briefing on it.
Samples
112 samples: 56 conditions, mostly in duplicateGroups 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
Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cellsNature genetics · 2024
Summary (written by the submitters)
Epigenetic treatment induces TE-chimeric antigens in glioblastoma stem cells
Published in
Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells
Jang HJ, Shah NM, Maeng JH et al. · Nature genetics 2024 · PMID 39223316 · doi:10.1038/s41588-024-01880-x
This dataset
Open GSE227059 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 GSE227059_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 peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA942972 and SRA study SRP426514. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39223316) ↗
Study design
56 conditions, mostly in duplicate
B36 cells, WGBS, DACPano, B ×2 B36 cells, WGBS, DMSO, B ×2 B49 cells, WGBS, DACPano, B ×2 B49 cells, WGBS, DMSO, B ×2 B66 cells, WGBS, DACPano, B ×2 B66 cells, WGBS, DMSO, B ×2 hFB cells, WGBS, DACPano, B ×2 hFB cells, WGBS, DMSO, B ×2 +48 more

Supports a between-group comparison across 112 samples.

How we read this: 56 replicated groups read from 112 sample titles; they account for 112 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

+ 72 more — browse all 112 samples with per-sample file links →

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.