TWEAK/Fn14 signalling in Breast Cancer [cell line 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: 8 conditions, mostly in triplicateGroups 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 GSE231479_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 PRJNA966128 and SRA study SRP435563. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 8 replicated groups read from 24 sample titles; they account for 20 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.
- GSM7286588 MB231_UT_K27_rep1 MB231_UT_K27
- GSM7286589 MB231_UT_K27_rep2 MB231_UT_K27
- GSM7286590 MB231_UT_K27_rep3 MB231_UT_K27
- GSM7286591 MB231_TWEAK_K27_rep1 MB231_TWEAK_K27
- GSM7286592 MB231_TWEAK_K27_rep2 MB231_TWEAK_K27
- GSM7286593 MB231_TWEAK_K27_rep3 MB231_TWEAK_K27
- GSM7286594 MB231_input
- GSM7286595 Hs578T_UT_K27_rep1 Hs578T_UT_K27
- GSM7286596 Hs578T_UT_K27_rep2 Hs578T_UT_K27
- GSM7286597 Hs578T_UT_K27_rep3 Hs578T_UT_K27
- GSM7286598 Hs578T_TWEAK_K27_rep1 Hs578T_TWEAK_K27
- GSM7286599 Hs578T_TWEAK_K27_rep2 Hs578T_TWEAK_K27
- GSM7286600 Hs578T_TWEAK_K27_rep3 Hs578T_TWEAK_K27
- GSM7286601 Hs578T_input
- GSM7286602 MCF7_UT_K27_rep1 MCF7_UT_K27
- GSM7286603 MCF7_UT_K27_rep2 MCF7_UT_K27
- GSM7286604 MCF7_TWEAK1_K27_rep1 MCF7_TWEAK1_K27
- GSM7286605 MCF7_TWEAK1_K27_rep2 MCF7_TWEAK1_K27
- GSM7286606 MCF7_input
- GSM7286607 CAMA1_UT_K27_rep1 CAMA1_UT_K27
- GSM7286608 CAMA1_UT_K27_rep2 CAMA1_UT_K27
- GSM7286609 CAMA1_TWEAK1_K27_rep1 CAMA1_TWEAK1_K27
- GSM7286610 CAMA1_TWEAK1_K27_rep2 CAMA1_TWEAK1_K27
- GSM7286611 CAMA1_input
- GSE289805 Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq] 126 samples shares breast, line, chip
- GSE329231 Epigenomic profiling of H3K9me3 and H3K27ac across melanoma cell lines with different mutational backgrounds 45 samples shares k27, line
- GSE289004 Mitochondrial calcium uniporter links acetyl-CoA metabolism and H3K27 acetylation to maintain glioblastoma stem cells [ChIP-Seq] 12 samples shares k27, 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
- GSE25066 Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 508 samples shares breast, line
- GSE25065 Validation cohort for genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer 198 samples shares breast, line
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.