TWEAK/Fn14 signalling in Breast Cancer [patient K27 ChIP]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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
- 24 samples: 24 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
- 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 GSE231482_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 PRJNA966129 and SRA study SRP435569. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 12 samples read as cases, 12 as controls.
How we read this: Read from 24 sample titles: 24 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.
- GSM7286648 z2086_Tumour_K27
- GSM7286649 z2086_Normal_K27
- GSM7286650 z8370_Tumour_K27
- GSM7286651 z8370_Normal_K27
- GSM7286652 z2963_Tumour_K27
- GSM7286653 z2963_Normal_K27
- GSM7286654 z6122_Tumour_K27
- GSM7286655 z6122_Normal_K27
- GSM7286656 z8850_Tumour_K27
- GSM7286657 z8850_Normal_K27
- GSM7286658 z5929_Tumour_K27
- GSM7286659 z5929_Normal_K27
- GSM7286660 z2086_Tumour_input
- GSM7286661 z2086_Normal_input
- GSM7286662 z8370_Tumour_input
- GSM7286663 z8370_Normal_input
- GSM7286664 z2963_Tumour_input
- GSM7286665 z2963_Normal_input
- GSM7286666 z6122_Tumour_input
- GSM7286667 z6122_Normal_input
- GSM7286668 z8850_Tumour_input
- GSM7286669 z8850_Normal_input
- GSM7286670 z5929_Tumour_input
- GSM7286671 z5929_Normal_input
- GSE289004 Mitochondrial calcium uniporter links acetyl-CoA metabolism and H3K27 acetylation to maintain glioblastoma stem cells [ChIP-Seq] 12 samples shares k27, chip
- GSE289805 Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq] 126 samples shares breast, chip
- GSE298767 Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [ChIP-seq] 63 samples shares breast, chip
- GSE259248 ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer (ChIP-Seq) 36 samples shares breast, chip
- GSE266407 ESR1 fusions invoke breast cancer subtype-dependent enrichment of ligand independent oncogenic signatures and phenotypes [ChIP-seq] 14 samples shares breast, chip
- GSE294321 Thyroid cancer-associated EZH1 Q571R mutation drives chromatin compaction and H3K27me3 invasion into active chromatin 16 samples shares k27
- GSE267119 The transcription factor ZNF469 regulates collagen production in liver fibrosis [Cohort_CUTRUN_H3K27ac] 99 samples shares k27
- GSE329231 Epigenomic profiling of H3K9me3 and H3K27ac across melanoma cell lines with different mutational backgrounds 45 samples shares k27
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.