TWEAK/Fn14 signalling in Breast Cancer [cell line ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 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
- 14 samples: 6 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 GSE231477_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 PRJNA966126 and SRA study SRP435566. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 6 replicated groups read from 14 sample titles; they account for 14 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.
- GSM7286570 MB231_UT_ATAC_rep1 MB231_UT_ATAC
- GSM7286571 MB231_UT_ATAC_rep2 MB231_UT_ATAC
- GSM7286572 MB231_UT_ATAC_rep3 MB231_UT_ATAC
- GSM7286573 MB231_TWEAK_ATAC_rep1 MB231_TWEAK_ATAC
- GSM7286574 MB231_TWEAK_ATAC_rep2 MB231_TWEAK_ATAC
- GSM7286575 MB231_TWEAK_ATAC_rep3 MB231_TWEAK_ATAC
- GSM7286576 Hs578T_UT_ATAC_rep1 Hs578T_UT_ATAC
- GSM7286577 Hs578T_UT_ATAC_rep2 Hs578T_UT_ATAC
- GSM7286578 Hs578T_TWEAK_ATAC_rep1 Hs578T_TWEAK_ATAC
- GSM7286579 Hs578T_TWEAK_ATAC_rep2 Hs578T_TWEAK_ATAC
- GSM7286580 MCF7_UT_ATAC_rep1 MCF7_UT_ATAC
- GSM7286581 MCF7_UT_ATAC_rep2 MCF7_UT_ATAC
- GSM7286582 MCF7_TWEAK_ATAC_rep1 MCF7_TWEAK_ATAC
- GSM7286583 MCF7_TWEAK_ATAC_rep2 MCF7_TWEAK_ATAC
- GSE289805 Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq] 126 samples shares atac-seq, breast, line
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares atac-seq, breast
- 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
- GSE248132 LARP6 promotes carcinogenic features of triple negative breast cancer cell line by directly modulating alternative splicing of associated genes 10 samples shares breast, line
- GSE308846 Reprogramming lineage features promotes epithelial behavior in carcinoma cells [ATAC-seq] 6 samples shares atac-seq, line
- GSE291679 Lineage Tracing Reveals Clone-Specific Responses to Doxorubicin in Triple-Negative Breast Cancer 36 samples shares breast, line
- GSE298767 Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [ChIP-seq] 63 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.