GEO series

Effects of Normoxia, Hypoxia, Oscillatory Hypoxia, and Lactate on Wild-Type, NOTCH1-Knockdown, and TP53-Knockdown MDA-MB-231 Cells

GSE292924 Homo sapiens (human) RNA-seq (gene expression) 36 samples Submitted 2025/10/27 Platform GPL34281

At a glance

RNA-seq (gene expression) · human · 36 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: 36 samples: 12 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.
Paper: Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancersNPJ systems biology and applications · 2025

Summary (written by the submitters)

Wild-type, NOTCH1-knockdown, and TP53-knockdown MDA-MB-231 cells were cultured under normoxia, hypoxia, oscillatory hypoxia, and lactate treatment, and subjected to RNA sequencing to assess transcriptional changes.

Published in

Hif-1 responsive IFFLs to explain specific transcriptional responses to cycling hypoxia in cancers

Qiu X, Liu Y, Vera-Licona P et al. · NPJ systems biology and applications 2025 · PMID 41285961 · doi:10.1038/s41540-025-00612-z

This dataset

Open GSE292924 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 GSE292924_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 PRJNA1241882 and SRA study SRP573072. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41285961) ↗

Study design

12 conditions, mostly in triplicate

Wild-type sample, normoxia condition, ×3 Wild-type sample, hypoxia condition, ×3 Wild-type sample, lactate condition, ×3 Wild-type sample, oscillatory hypoxia conditi… ×3 NOTCH1 knock-down sample, normoxia condition, ×3 NOTCH1 knock-down sample, hypoxia condition, ×3 NOTCH1 knock-down sample, lactate condition, ×3 NOTCH1 knock-down sample, oscillatory hypoxi… ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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

GSM8869487 Wild-type sample, normoxia condition, replicate 1 Wild-type sample, normo…
GSM8869488 Wild-type sample, normoxia condition, replicate 2 Wild-type sample, normo…
GSM8869489 Wild-type sample, normoxia condition, replicate 3 Wild-type sample, normo…
GSM8869490 Wild-type sample, hypoxia condition, replicate 1 Wild-type sample, hypox…
GSM8869491 Wild-type sample, hypoxia condition, replicate 2 Wild-type sample, hypox…
GSM8869492 Wild-type sample, hypoxia condition, replicate 3 Wild-type sample, hypox…
GSM8869493 Wild-type sample, lactate condition, replicate 1 Wild-type sample, lacta…
GSM8869494 Wild-type sample, lactate condition, replicate 2 Wild-type sample, lacta…
GSM8869495 Wild-type sample, lactate condition, replicate 3 Wild-type sample, lacta…
GSM8869496 Wild-type sample, oscillatory hypoxia condition, replicate 1 Wild-type sample, oscil…
GSM8869497 Wild-type sample, oscillatory hypoxia condition, replicate 2 Wild-type sample, oscil…
GSM8869498 Wild-type sample, oscillatory hypoxia condition, replicate 3 Wild-type sample, oscil…
GSM8869499 NOTCH1 knock-down sample, normoxia condition, replicate 1 NOTCH1 knock-down sampl…
GSM8869500 NOTCH1 knock-down sample, normoxia condition, replicate 2 NOTCH1 knock-down sampl…
GSM8869501 NOTCH1 knock-down sample, normoxia condition, replicate 3 NOTCH1 knock-down sampl…
GSM8869502 NOTCH1 knock-down sample, hypoxia condition, replicate 1 NOTCH1 knock-down sampl…
GSM8869503 NOTCH1 knock-down sample, hypoxia condition, replicate 2 NOTCH1 knock-down sampl…
GSM8869504 NOTCH1 knock-down sample, hypoxia condition, replicate 3 NOTCH1 knock-down sampl…
GSM8869505 NOTCH1 knock-down sample, lactate condition, replicate 1 NOTCH1 knock-down sampl…
GSM8869506 NOTCH1 knock-down sample, lactate condition, replicate 2 NOTCH1 knock-down sampl…
GSM8869507 NOTCH1 knock-down sample, lactate condition, replicate 3 NOTCH1 knock-down sampl…
GSM8869508 NOTCH1 knock-down sample, oscillatory hypoxia condition, replicate 1 NOTCH1 knock-down sampl…
GSM8869509 NOTCH1 knock-down sample, oscillatory hypoxia condition, replicate 2 NOTCH1 knock-down sampl…
GSM8869510 NOTCH1 knock-down sample, oscillatory hypoxia condition, replicate 3 NOTCH1 knock-down sampl…
GSM8869511 TP53 knock-down sample, normoxia condition, replicate 1 TP53 knock-down sample,…
GSM8869512 TP53 knock-down sample, normoxia condition, replicate 2 TP53 knock-down sample,…
GSM8869513 TP53 knock-down sample, normoxia condition, replicate 3 TP53 knock-down sample,…
GSM8869514 TP53 knock-down sample, hypoxia condition, replicate 1 TP53 knock-down sample,…
GSM8869515 TP53 knock-down sample, hypoxia condition, replicate 2 TP53 knock-down sample,…
GSM8869516 TP53 knock-down sample, hypoxia condition, replicate 3 TP53 knock-down sample,…
GSM8869517 TP53 knock-down sample, lactate condition, replicate 1 TP53 knock-down sample,…
GSM8869518 TP53 knock-down sample, lactate condition, replicate 2 TP53 knock-down sample,…
GSM8869519 TP53 knock-down sample, lactate condition, replicate 3 TP53 knock-down sample,…
GSM8869520 TP53 knock-down sample, oscillatory hypoxia condition, replicate 1 TP53 knock-down sample,…
GSM8869521 TP53 knock-down sample, oscillatory hypoxia condition, replicate 2 TP53 knock-down sample,…
GSM8869522 TP53 knock-down sample, oscillatory hypoxia condition, replicate 3 TP53 knock-down sample,…

Datasets on a similar topic

GSE261312 Effect of Hypoxia, Oscillatory Hypoxia, and Lactate on MDA 231 Cells 12 samples shares oscillatory, hypoxia, lactate
GSE253047 mRNA sequencing of MDA-MB-231 engineered for doxycycline-inducible overexpression of wild-type or mutant myocardin related transcription factor A 24 samples shares mda-mb-231, wild-type
GSE297242 Effect of lactate accumulation on translation and transcription in MDA-MB-231 breast cancer cells 12 samples shares mda-mb-231, lactate
GSE266011 Effect of CRY2 stabilizer and proteasome inhibitor on the transcription of MDA-MB-231 cells [RNA-seq] 36 samples shares mda-mb-231
GSE336730 RNA-seq analysis of MDA-MB-231 and MDA-MB-453 cells treated with abemaciclib and/or fulvestrant 24 samples shares mda-mb-231
GSE282896 Ferroptosis Induced by Omega-3 Docosahexaenoic Acid (DHA) and Erastin in Control MDA-MB-231 Cells (sh-LUC) and MDA-MB-231 Cells with knockdown of IGFBP6 gene (sh-IGFBP6) 18 samples shares mda-mb-231
GSE271120 TRAIL-induced cytokine production via NFKB2 pathway promotes neutrophil chemotaxis and immune suppression in triple negative breast cancers [MDA-MB-231] 17 samples shares mda-mb-231
GSE299393 Single cell RNAseq dataset of MDA-MB-231 xenograft and matched metastasis 17 samples shares mda-mb-231

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.