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RNA-seq profiling of osteosarcoma and healthy bone samples from a Central Mexican cohort

GSE337651 Homo sapiens (human) RNA-seq (gene expression) 14 samples Submitted 2026/08/05 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 14 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
OsteosarcomaThis series is part of our curated briefing on it.
Samples
14 samples: 7 × Osteosarcoma tumor sample vs 7 × Healthy bone reference sampleGroups 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
Integrative Transcriptomic and Network Analysis of Shared Osteo-Immune Regulatory Programs in Postmenopausal Osteoporosis and Osteosarcoma Within Central Mexican CohortsCurrent issues in molecular biology · 2026
Summary (written by the submitters)
This bulk RNA-seq dataset contains transcriptomic profiles from osteosarcoma tumor samples and healthy bone reference samples from a Central Mexican cohort. Gene-level raw count and TPM-normalized expression matrices were generated from paired-end RNA-seq reads processed through a standardized quality-control, alignment, and quantification workflow. The dataset supports analyses of differential gene expression and molecular pathways involved in osteosarcoma biology, bone remodeling, extracellular matrix organization, immune regulation, and osteo-immune programs.
Published in
Integrative Transcriptomic and Network Analysis of Shared Osteo-Immune Regulatory Programs in Postmenopausal Osteoporosis and Osteosarcoma Within Central Mexican Cohorts
Jiménez-Ortega RF, de la Cruz-Montoya AH, Patiño N et al. · Current issues in molecular biology 2026 · PMID 42510987 · doi:10.3390/cimb48070747
This dataset
Open GSE337651 in finder → Find more human RNA-seq datasets → Osteosarcoma 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 GSE337651_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 PRJNA1490546 and SRA study SRP715521. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42510987) ↗
Study design
7 × Osteosarcoma tumor sample vs 7 × Healthy bone reference sample

Supports a case/control comparison: 7 samples read as cases, 7 as controls.

How we read this: 2 replicated groups read from 14 sample titles; they account for 14 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 Osteosarcoma 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.