p53 drives epigenetic programs associated with luminal cell identity in breast cancer [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
- 12 samples: 3 × ATACseq_MCF7_WT_NT vs 3 × ATACseq_MCF7_WT_Tam vs 3 × ATACseq_MCF7_KO_NT vs 3 × ATACseq_MCF7_KO_TamGroups 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
- p53 regulates the expression of histone modifiers to restrict stemness and maintain differentiated luminal identity in breast cancerProceedings of the National Academy of Sciences of the United States of America · 2025
Read the full summary ↓
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 GSE292361_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 PRJNA1238236 and SRA study SRP571696. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8857468 ATACseq_MCF7_WT_NT_rep1 ATACseq_MCF7_WT_NT
- GSM8857469 ATACseq_MCF7_WT_NT_rep2 ATACseq_MCF7_WT_NT
- GSM8857470 ATACseq_MCF7_WT_NT_rep3 ATACseq_MCF7_WT_NT
- GSM8857471 ATACseq_MCF7_WT_Tam_rep1 ATACseq_MCF7_WT_Tam
- GSM8857472 ATACseq_MCF7_WT_Tam_rep2 ATACseq_MCF7_WT_Tam
- GSM8857473 ATACseq_MCF7_WT_Tam_rep3 ATACseq_MCF7_WT_Tam
- GSM8857474 ATACseq_MCF7_KO_NT_rep1 ATACseq_MCF7_KO_NT
- GSM8857475 ATACseq_MCF7_KO_NT_rep2 ATACseq_MCF7_KO_NT
- GSM8857476 ATACseq_MCF7_KO_NT_rep3 ATACseq_MCF7_KO_NT
- GSM8857477 ATACseq_MCF7_KO_Tam_rep1 ATACseq_MCF7_KO_Tam
- GSM8857478 ATACseq_MCF7_KO_Tam_rep2 ATACseq_MCF7_KO_Tam
- GSM8857479 ATACseq_MCF7_KO_Tam_rep3 ATACseq_MCF7_KO_Tam
- 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
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares epigenetic, luminal
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares atac-seq, breast
- GSE243526 Defining the Regulatory Logic of Breast Cancer Using Single-Cell Epigenetic and Transcriptome Profiling 40 samples shares epigenetic, breast
- GSE323981 MEF2C controls lysosomal and lipid clearance programs linked to Alzheimer’s disease risk in macrophages [ATAC-seq] 8 samples shares programs, atac-seq
- GSE316079 SLF2 and SMC5 dysfunction drives HSC aging and predisposes to MDS, defining a new inherited bone marrow failure syndrome [ATAC-seq] 6 samples shares atac-seq, drives
- GSE277909 Epigenetic attenuation of interferon signaling drives aging-related improvements in systemic lupus 271 samples shares epigenetic, drives
- GSE270503 Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [Cut&Run] 56 samples shares epigenetic, programs
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.