TWEAK/Fn14 signalling in Breast Cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 64 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Homo sapiens (human)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 64 samples: 29 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
- TWEAK/Fn14 signalling driven super-enhancer reprogramming promotes pro-metastatic metabolic rewiring in triple-negative breast cancerNature communications · 2024
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 GSE231483_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA966116 and SRA study SRP479506. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 62 samples.
How we read this: 29 replicated groups read from 64 sample titles; they account for 62 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.
- GSM7989287 MB231_control_K27_UT1 MB231_control_K27_UT
- GSM7989288 MB231_control_K27_UT2 MB231_control_K27_UT
- GSM7989289 MB231_control_K27_TW1 MB231_control_K27_TW
- GSM7989290 MB231_control_K27_TW2 MB231_control_K27_TW
- GSM7989291 MB231_Fn14KO_K27_UT1 MB231_Fn14KO_K27_UT
- GSM7989292 MB231_Fn14KO_K27_UT2 MB231_Fn14KO_K27_UT
- GSM7989293 MB231_Fn14KO_K27_TW1 MB231_Fn14KO_K27_TW
- GSM7989294 MB231_Fn14KO_K27_TW2 MB231_Fn14KO_K27_TW
- GSM7989295 Hs578T_control_K27_UT1 Hs578T_control_K27_UT
- GSM7989296 Hs578T_control_K27_UT2 Hs578T_control_K27_UT
- GSM7989297 Hs578T_control_K27_TW1 Hs578T_control_K27_TW
- GSM7989298 Hs578T_control_K27_TW2 Hs578T_control_K27_TW
- GSM7989299 Hs578T_Fn14KO_K27_UT1 Hs578T_Fn14KO_K27_UT
- GSM7989300 Hs578T_Fn14KO_K27_UT2 Hs578T_Fn14KO_K27_UT
- GSM7989301 Hs578T_Fn14KO_K27_TW1 Hs578T_Fn14KO_K27_TW
- GSM7989302 Hs578T_Fn14KO_K27_TW2 Hs578T_Fn14KO_K27_TW
- GSM7989303 SKBR3_UT_MAFG_rep1 SKBR3_UT_MAFG
- GSM7989304 SKBR3_UT_MAFG_rep2 SKBR3_UT_MAFG
- GSM7989305 SKBR3_TWEAK_MAFG_rep1 SKBR3_TWEAK_MAFG
- GSM7989306 SKBR3_TWEAK_MAFG_rep2 SKBR3_TWEAK_MAFG
- GSM7989307 MCF7_UT_MAFG_rep1 MCF7_UT_MAFG
- GSM7989308 MCF7_UT_MAFG_rep2 MCF7_UT_MAFG
- GSM7989309 MCF7_TWEAK_MAFG_rep1 MCF7_TWEAK_MAFG
- GSM7989310 MCF7_TWEAK_MAFG_rep2 MCF7_TWEAK_MAFG
- GSM7989311 MB231_UT_MAFG_rep1 MB231_UT_MAFG
- GSM7989312 MB231_UT_MAFG_rep2 MB231_UT_MAFG
- GSM7989313 MB231_TWEAK_MAFG_rep1 MB231_TWEAK_MAFG
- GSM7989314 MB231_TWEAK_MAFG_rep2 MB231_TWEAK_MAFG
- GSM7989315 Hs578T_UT_MAFG_rep1 Hs578T_UT_MAFG
- GSM7989316 Hs578T_UT_MAFG_rep2 Hs578T_UT_MAFG
- GSM7989317 Hs578T_TWEAK_MAFG_rep1 Hs578T_TWEAK_MAFG
- GSM7989318 Hs578T_TWEAK_MAFG_rep2 Hs578T_TWEAK_MAFG
- GSM7989319 SKBR3_UT_K27_rep1 SKBR3_UT_K27
- GSM7989320 SKBR3_UT_K27_rep2 SKBR3_UT_K27
- GSM7989321 SKBR3_TWEAK_K27_rep1 SKBR3_TWEAK_K27
- GSM7989322 SKBR3_TWEAK_K27_rep2 SKBR3_TWEAK_K27
- GSM7989323 SKBR3_input
- GSM7989324 MB453_UT_K27_rep1 MB453_UT_K27
- GSM7989325 MB453_UT_K27_rep2 MB453_UT_K27
- GSM7989326 MB453_TWEAK_K27_rep1 MB453_TWEAK_K27
+ 24 more — browse all 64 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
- 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
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 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
- GSE283522 The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer 1254 samples shares breast
- GSE25066 Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 508 samples shares breast
- GSE319641 RNA-Seq profiling of pre- and on-treatment tumor samples from breast cancer patients enrolled in the NeoTRIP trial. 401 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.