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An integrated clinical genomic and transcriptomic subgrouping of central chondrosarcoma

GSE299759 Homo sapiens (human) RNA-seq (gene expression) 54 samples Submitted 2026/01/04 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 54 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
54 samples
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
An Integrated Clinical Genomic and Transcriptomic Subgrouping of Central ChondrosarcomaModern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2025
Summary (written by the submitters)
Chondrosarcoma, a malignant cartilage-producing bone tumor, is the second most-common bone sarcoma. Chondrosarcomas are histologically graded, which is so far the best predictor of survival. Early mutations in isocitrate dehydrogenase (IDH)-1 and -2 genes are frequent, leading to the production of the oncometabolite D-2-hydroxyglutarate, which affects DNA methylation, resulting in a preferred chondrogenic differentiation over osteogenic differentiation of mesenchymal stem cells, which are currently considered the precursor cells of chondrosarcomas.
Read the full summary ↓
DNA methylation profiling has previously revealed distinct profiles between IDH mutant and wild-type chondrosarcomas, but the presence of further DNA methylation subgroups indicates that classification based solely on IDH status is too simplistic. In this study, we aim to identify biological subgroups in chondrosarcomas by combining clinical data, IDH mutation status, gene expression and genome wide loss of heterozygosity (gwLOH).
Published in
An Integrated Clinical Genomic and Transcriptomic Subgrouping of Central Chondrosarcoma
Meijer DM, Venneker S, Ameline B et al. · Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc 2025 · PMID 40976495 · doi:10.1016/j.modpat.2025.100894
This dataset
Open GSE299759 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 GSE299759_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 PRJNA1276455 and SRA study SRP591871. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40976495) ↗
Study design
A cohort of 54 individual samples

The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Sample titles run L0795 … L7851 and carry no group information.

Samples in this study

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

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.