Effect of depletion of hypoxia-inducible factor (HIFs) on gene expression in MDA231-BrM2 breast cancer brain-selective metastatic cells with RNA-Seq.
RNA-seq (gene expression) · human · 12 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
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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 promotes murine breast cancer brain metastasis by increasing production of integrin β3-containing extracellular vesiclesThe Journal of clinical investigation · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE268804_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1118773 and SRA study SRP511066. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 12 sample titles: 12 distinct titles with little repetition. 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.
- GSM8299684 MDA231-BrM2 cells, NTC, 20% O2 (biol rep 1)
- GSM8299685 MDA231-BrM2 cells, NTC, 20% O2 (biol rep 2)
- GSM8299686 MDA231-BrM2 cells, NTC, 20% O2 (biol rep 3)
- GSM8299687 MDA231-BrM2 cells, NTC, 1% O2 (biol rep 1)
- GSM8299688 MDA231-BrM2 cells, NTC, 1% O2 (biol rep 2)
- GSM8299689 MDA231-BrM2 cells, NTC, 1% O2 (biol rep 3)
- GSM8299690 MDA231-BrM2 cells, DKD, 20% O2 (biol rep 1)
- GSM8299691 MDA231-BrM2 cells, DKD, 20% O2 (biol rep 2)
- GSM8299692 MDA231-BrM2 cells, DKD, 20% O2 (biol rep 3)
- GSM8299693 MDA231-BrM2 cells, DKD, 1% O2 (biol rep 1)
- GSM8299694 MDA231-BrM2 cells, DKD, 1% O2 (biol rep 2)
- GSM8299695 MDA231-BrM2 cells, DKD, 1% O2 (biol rep 3)
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing · shares breast
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares breast
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing · shares breast
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares breast
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE316391 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [RNA-seq] 32 samples shares metastatic, rna-seq, breast
- GSE281580 Human scRNA-seq of three primary and five metastatic breast cancers 8 samples shares metastatic, rna-seq, breast
- GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares metastatic, rna-seq
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.