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Differential gene expressions of cancer cells cultured in an oxygen-limiting, micro-metabolic rewiring (μMeRe) device over their normoxia control

GSE265781 Homo sapiens (human) RNA-seq (gene expression) 32 samples Submitted 2025/02/27 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 32 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
32 samples: 16 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
A micro-metabolic rewiring assay for assessing hypoxia-associated cancer metabolic heterogeneityBioactive materials · 2025
Summary (written by the submitters)
Cancer metabolism plays an essential role in therapeutic resistance, where significant inter- and intra-tumoral heterogeneity exists. Hypoxia is a prominent driver of metabolic rewiring behaviors and drug responses. Recapitulating the hypoxic landscape in tumor microenvironment thus offers unique insights into heterogeneity in metabolic rewiring and therapeutic responses, to inform better treatment strategies.
Read the full summary ↓
We developed a micro-metabolic rewiring (μMeRe) device that provides the scalability and resolution needed to characterize the metabolic rewiring behaviors of different cancer cells in the context of hypoxic solid tumors. Our device generates hypoxia through cellular metabolism without external gas controls, enabling the characterization of cell-specific intrinsic ability to drive hypoxia and undergo metabolic rewiring. We assessed the changes in the transcriptomic profile of different cancer cells in the μMeRe device compared to their normoxia counterpart through bulk RNA-seq. Our data confirms heterogeneity and commonality of rewiring behaviors of diverse cancer cell types.
Published in
A micro-metabolic rewiring assay for assessing hypoxia-associated cancer metabolic heterogeneity
Oh JM, Guo T, Begum HM et al. · Bioactive materials 2025 · PMID 40093303 · doi:10.1016/j.bioactmat.2025.02.030
This dataset
Open GSE265781 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 GSE265781_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 PRJNA1104187 and SRA study SRP503804. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40093303) ↗
Study design
16 conditions, mostly in duplicate
A549 cells, µMeRe device (hypoxic), 24 hr, ×2 A549 cells, normoxic device, 24 hr, ×2 PC9 cells, µMeRe device (hypoxic), 24 hr, ×2 PC9 cells, normoxic device, 24 hr, ×2 LNCaP cells, µMeRe device (hypoxic), 24 hr, ×2 LNCaP cells, normoxic device, 24 hr, ×2 PC3 cells, µMeRe device (hypoxic), 24 hr, ×2 PC3 cells, normoxic device, 24 hr, ×2 +8 more

Supports a between-group comparison across 32 samples.

How we read this: 16 replicated groups read from 32 sample titles; they account for 32 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
Datasets on a similar topic

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