Interaction of BCL11A and CHD8 in triple negative breast cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 22 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
- Mus musculus (mouse)
- Samples
- 22 samples: 22 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
- CHD8 interacts with BCL11A to induce oncogenic transcription in triple negative breast cancerThe EMBO journal · 2025
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 GSE174187_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 PRJNA728695 and SRA study SRP319207. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 22 sample titles: 22 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.
- GSM5288644 4T1 cells, control_rep1 (ATACseq)
- GSM5288645 4T1 cells, control_rep2 (ATACseq)
- GSM5288646 4T1 cells, 11A_rep1 (ATACseq)
- GSM5288647 4T1 cells, 11A_rep2 (ATACseq)
- GSM5288648 4T1 cells, CHD8_rep1 (ATACseq)
- GSM5288649 4T1 cells, CHD8_rep2 (ATACseq)
- GSM5288694 4T1 cells, control_11A_IP (ChIPseq)
- GSM5288695 4T1 cells, control_CHD8_IP (ChIPseq)
- GSM5288696 4T1 cells, 11A_KD_11A_IP (ChIPseq)
- GSM5288697 4T1 cells, 11A_KD_CHD8_IP (ChIPseq)
- GSM5288698 4T1 cells, CHD8_KD_11A_IP (ChIPseq)
- GSM5288699 4T1 cells, CHD8_KD_CHD8_IP (ChIPseq)
- GSM5288700 4T1 cells, input:7c (ChIPseq)
- GSM5288719 4T1 cells, control_rep1 (RNAseq)
- GSM5288720 4T1 cells, 11A_rep1 (RNAseq)
- GSM5288721 4T1 cells, CHD8_rep1 (RNAseq)
- GSM5288722 4T1 cells, control_rep2 (RNAseq)
- GSM5288723 4T1 cells, 11A_rep2 (RNAseq)
- GSM5288724 4T1 cells, CHD8_rep2 (RNAseq)
- GSM5288725 4T1 cells, control_rep3 (RNAseq)
- GSM5288726 4T1 cells, 11A_rep3 (RNAseq)
- GSM5288727 4T1 cells, CHD8_rep3 (RNAseq)
- GSE311488 Chemotherapeutic Induction of Single-Stranded DNA Accumulation Sensitizes Triple-Negative Breast Cancer to Immunotherapy [scRNA-seq] 32 samples shares negative, triple, breast
- GSE294999 Obesity-driven inflammation enables triple-negative breast cancer progression through immunosuppression [scRNA-Seq] 16 samples shares negative, triple, breast
- GSE317281 Integrated bulk and single-cell transcriptome analysis reveals the impact of cyclophosphamide on tumor microenvironment in triple-negative breast cancer models 14 samples shares negative, triple, breast
- GSE263255 FXR Agonism with Bile Acid Mimetic Reduces Pre-Clinical Triple-Negative Breast Cancer Burden 13 samples shares negative, triple, breast
- GSE249759 In vivo CRISPR screens identify Mga as an immunotherapy target in triple-negative breast cancer 12 samples shares negative, triple, breast
- GSE304626 The CXCL10/CXCR3 axis is essential for sustaining immunological dormancy in triple-negative breast cancer 12 samples shares negative, triple, breast
- GSE267535 TLR4-dependent fibroblast-monocyte axis in tumor-draining lymph nodes contributes to metastasis in triple-negative breast cancer 10 samples shares negative, triple, breast
- GSE341921 PGK1 moonlights as an NF-kB/p65 kinase to orchestrate M2-like macrophage-mediated immunosuppression in triple-negative breast cancer 6 samples shares negative, triple, 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.