Expression profiling by high throughput sequencing of breast cancer
RNA-seq (gene expression) · human · 158 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
- 158 samples: 94 × A vs 64 × BGroups 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
- Quantitative coupling of clonal CNV evolution and spatially restricted malignant states identifies MFGE8 as a candidate late-state-associated target in breast cancerJournal of translational medicine · 2026
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 GSE323973_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 PRJNA1432817. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 158 samples.
How we read this: 2 replicated groups read from 158 sample titles; they account for 158 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.
- GSM9565777 A_001 A
- GSM9565778 A_002 A
- GSM9565779 A_003 A
- GSM9565780 A_005 A
- GSM9565781 A_006 A
- GSM9565782 A_007 A
- GSM9565783 A_008 A
- GSM9565784 A_009 A
- GSM9565785 A_012 A
- GSM9565786 A_013 A
- GSM9565787 A_014 A
- GSM9565788 A_015 A
- GSM9565789 A_016 A
- GSM9565790 A_017 A
- GSM9565791 A_018 A
- GSM9565792 A_019 A
- GSM9565793 A_020 A
- GSM9565794 A_021 A
- GSM9565795 A_022 A
- GSM9565796 A_023 A
- GSM9565797 A_024 A
- GSM9565798 A_026 A
- GSM9565799 A_027 A
- GSM9565800 A_028 A
- GSM9565801 A_029 A
- GSM9565802 A_030 A
- GSM9565803 A_031 A
- GSM9565804 A_032 A
- GSM9565805 A_033 A
- GSM9565806 A_034 A
- GSM9565807 A_035 A
- GSM9565808 A_036 A
- GSM9565809 A_038 A
- GSM9565810 A_039 A
- GSM9565811 A_040 A
- GSM9565812 A_041 A
- GSM9565813 A_042 A
- GSM9565814 A_043 A
- GSM9565815 A_044 A
- GSM9565816 A_045 A
+ 118 more — browse all 158 samples with per-sample file links →
- 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
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 samples shares breast
- GSE316391 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [RNA-seq] 32 samples shares breast
- GSE283522 The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer 1254 samples shares breast
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.