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Gene expression profile of Radiatiom resistant BRAFV400E type pediatric low-grade gliomas

GSE268207 Homo sapiens (human) RNA-seq (gene expression) 60 samples Submitted 2026/05/22 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 60 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)
Samples
60 samples: 20 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)
Inhibitors of the MAPK pathway (MAPKi) have shown significant activity in treatment of childhood BRAF-activated brain tumors. However, for tumors harboring BRAFV600E mutations, the drugs are rarely curative, and patients can become refractory to treatment. Combining MAPKi with low dose X-ray therapy (XRT) has the potential to improve the cure rate, but development of XRT resistance poses a major challenge.
Read the full summary ↓
To understand the mechanisms of radiation resistance in BRAFV600E type pediatric low-grade gliomas, radiation resistance models were developed by using BT-40 and IC-3635, two pediatric low-grade glioma (PLGG) PDX models BRAFV600E mutation. RNA sequencing was performed to determine the gene expression profile of primary tumors and resistant tumors, and their response to XRT treatment. Each tumor tissue was transplanted to 12 scid mice, respectively. Treatment was started when tumor volume reach ~0.3~0.6 cm3. Tumors on mice were exposed locally to single dose 5Gy X-radiatiom, and tumor tissue (from three mice, triplicates) were collected at 0 (no treatment), 2, 8 and 24 hours post treatment, and were snap-frozen in liquid nitrogen. RNA was isolated and applied to subsequent 100bp paired read sequencing run with Illumina NovaSeq 6000 platform at 100 bp paired-end module.
This dataset
Open GSE268207 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 GSE268207_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 PRJNA1115133 and SRA study SRP509436. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
20 conditions, mostly in triplicate
BT40-control, ×3 BT40-5Gy Xray 2hr, ×3 BT40-5Gy Xray 8hr, ×3 BT40-5Gy Xray 24hr, ×3 IC3635X-5Gy Xray 8hr, ×3 IC3635X-5Gy Xray 24hr, ×3 IC3635-control, ×3 IC3635-5Gy Xray 2hr, ×3 +14 more

Supports a between-group comparison across 58 samples.

How we read this: 20 replicated groups read from 60 sample titles; they account for 58 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

+ 20 more — browse all 60 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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