TWEAK/Fn14 signalling in Breast Cancer (MAFG ChIP-seq)
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 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)
- Samples
- 16 samples: 8 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 GSE251867_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 PRJNA1055580 and SRA study SRP479507. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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.
- 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
- GSE289805 Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq] 126 samples shares chip-seq, breast
- GSE261988 SWI/SNF is a gatekeeper of chromatin access at enhancer networks controlling triple-negative breast cancer progression [ChIP-Seq] 79 samples shares chip-seq, breast
- GSE298767 Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [ChIP-seq] 63 samples shares chip-seq, breast
- GSE271703 Integrated ChIP-seq and Transcriptomic Profiling of Histone Modifications Across Breast Cancer Progression in MCF10A-Derived Cell Lines [ChIP-Seq] 60 samples shares chip-seq, breast
- GSE259248 ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer (ChIP-Seq) 36 samples shares chip-seq, breast
- GSE241598 Proteasome inhibition reprograms chromatin landscape in breast cancer (ChIP-Seq) 18 samples shares chip-seq, breast
- GSE266407 ESR1 fusions invoke breast cancer subtype-dependent enrichment of ligand independent oncogenic signatures and phenotypes [ChIP-seq] 14 samples shares chip-seq, breast
- GSE280574 mChIP-seq for high-throughput epigenomic profiling reveals a decoupling of H2A.Z and H3K4me3 in cancer 576 samples shares chip-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.