GEO series
Combined inhibition of KAT6A/B and Menin reverses estrogen receptor-driven gene expression programs in breast cancer (ChIP-Seq)
GSE264726
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
69 samples
Submitted 2025/04/30
Platform GPL18573
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 69 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
- 69 samples: 69 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
- Combined inhibition of KAT6A/B and Menin reverses estrogen receptor-driven gene expression programs in breast cancerCell reports. Medicine · 2025
Summary (written by the submitters)
KAT6A is a histone acetyltransferase that is emerging as a therapeutic target in cancer, including estrogen receptor positive (ER+) breast cancer. We performed CRISPR screens to identify the chromatin adaptor Menin as a regulator of KAT6A inhibitor response. Co-treatment with KAT6A/B and Menin inhibitors had synergistic anti-proliferative effects in ER+, but not ER-, breast cancer lines.
Read the full summary ↓
Our data revealed that KAT6A and Menin cooperatively regulate ER-driven gene expression and chromatin accessibility via direct effects on ESR1 expression and at ER target genes. KAT6A and Menin co-localize at promoters of ESR1 and ER-driven genes and combined KAT6A/B and Menin inhibition selectively displaced RNA Pol II from chromatin at these loci. Combined KAT6A/B and Menin inhibition was effective in ER+ patient-derived organoids and in models of endocrine resistance. KAT6A/B and Menin inhibitors are currently in clinical trials and have shown manageable toxicity profiles, underscoring the potential therapeutic relevance for ER+ breast cancer.
Published in
Olsen SN, Anderson B, Hatton C et al.
· Cell reports. Medicine 2025
· PMID 40516531
· doi:10.1016/j.xcrm.2025.102192
This dataset
Download · which file do I need?
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.
1 · Just have a look
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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE264726_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
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 PRJNA1103854 and SRA study SRP503672. Searching any of these in the dataset finder brings you back here.
Study design
69 samples, each with a distinct title — no replicated groups
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 69 sample titles: 69 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.
Samples in this study
- GSM8226651 MCF7_ChIP_BRPF1_steadystate_REP1_230601_ACTTGA_S9_R1_merged.fastq.gz
- GSM8226652 MCF7_ChIP_H3K4me3_DMSO_REP1_231110_GTCCGC_S13_R1_merged.fastq.gz
- GSM8226653 MCF7_ChIP_H3K4me3_PF9363_50nM_REP1_231110_GTGAAA_S14_R1_merged.fastq.gz
- GSM8226654 MCF7_ChIP_H3K4me3_PF9363_50nM_SNDX_200nM_REP1_231110_GTTTCG_S16_R1_merged.fastq.gz
- GSM8226655 MCF7_ChIP_H3K4me3_SNDX_200nM_REP1_231110_GTGGCC_S15_R1_merged.fastq.gz
- GSM8226656 MCF7_ChIP_H3K9ac_DMSO_REP1_231110_CTTGTA_S9_R1_merged.fastq.gz
- GSM8226657 MCF7_ChIP_H3K9ac_PF9363_50nM_REP1_231110_AGTCAA_S10_R1_merged.fastq.gz
- GSM8226658 MCF7_ChIP_H3K9ac_PF9363_50nM_SNDX_200nM_REP1_231110_ATGTCA_S12_R1_merged.fastq.gz
- GSM8226659 MCF7_ChIP_H3K9ac_SNDX_200nM_REP1_231110_AGTTCC_S11_R1_merged.fastq.gz
- GSM8226660 MCF7_ChIP_input_DMSO_24h_REP1_231211_ATCACG_S1_R1_merged.fastq.gz
- GSM8226661 MCF7_ChIP_input_DMSO_5d_REP1_221012_GAGTGG_S11_R1_merged.fastq.gz
- GSM8226662 MCF7_ChIP_input_DMSO_REP1_231110_ATCACG_S1_R1_merged.fastq.gz
- GSM8226663 MCF7_ChIP_input_PF9363_50nM_24h_REP1_231211_CGATGT_S2_R1_merged.fastq.gz
- GSM8226664 MCF7_ChIP_input_PF9363_50nM_REP1_231110_CGATGT_S2_R1_merged.fastq.gz
- GSM8226665 MCF7_ChIP_input_PF9363_50nM_SNDX_200nM_24h_REP1_231211_TGACCA_S4_R1_merged.fastq.gz
- GSM8226666 MCF7_ChIP_input_PF9363_50nM_SNDX_200nM_REP1_231110_TGACCA_S4_R1_merged.fastq.gz
- GSM8226667 MCF7_ChIP_input_SNDX_200nM_24h_REP1_231211_TTAGGC_S3_R1_merged.fastq.gz
- GSM8226668 MCF7_ChIP_input_SNDX_200nM_REP1_231110_TTAGGC_S3_R1_merged.fastq.gz
- GSM8226669 MCF7_ChIP_input_steadystate_REP1_220531_TGACCA_S4_R1_merged.fastq.gz
- GSM8226670 MCF7_ChIP_input_steadystate_REP1_230601_ATCACG_S3_R1_merged.fastq.gz
- GSM8226671 MCF7_ChIP_input_VTP_200nM_5d_REP1_221012_ACTGAT_S12_R1_merged.fastq.gz
- GSM8226672 MCF7_ChIP_KAT6A_DMSO_24h_REP1_231211_AGTCAA_S13_R1_merged.fastq.gz
- GSM8226673 MCF7_ChIP_KAT6A_PF9363_50nM_24h_REP1_231211_AGTTCC_S14_R1_merged.fastq.gz
- GSM8226674 MCF7_ChIP_KAT6A_PF9363_50nM_SNDX_200nM_24h_REP1_231211_CCGTCC_S16_R1_merged.fastq.gz
- GSM8226675 MCF7_ChIP_KAT6A_SNDX_200nM_24h_REP1_231211_ATGTCA_S15_R1_merged.fastq.gz
- GSM8226676 MCF7_ChIP_KAT6A_steadystate_REP1_230601_ACAGTG_S6_R1_merged.fastq.gz
- GSM8226677 MCF7_ChIP_MEN1_DMSO_5d_REP1_221012_GGCTAC_S9_R1_merged.fastq.gz
- GSM8226678 MCF7_ChIP_MEN1_steadystate_REP1_220531_CGATGT_S2_R1_merged.fastq.gz
- GSM8226679 MCF7_ChIP_MEN1_VTP_200nM_5d_REP1_221012_CTTGTA_S10_R1_merged.fastq.gz
- GSM8226680 MCF7_ChIP_MLL1_DMSO_24h_REP1_231211_GATCAG_S9_R1_merged.fastq.gz
- GSM8226681 MCF7_ChIP_MLL1_PF9363_50nM_24h_REP1_231211_TAGCTT_S10_R1_merged.fastq.gz
- GSM8226682 MCF7_ChIP_MLL1_PF9363_50nM_SNDX_200nM_24h_REP1_231211_CTTGTA_S12_R1_merged.fastq.gz
- GSM8226683 MCF7_ChIP_MLL1_SNDX_200nM_24h_REP1_231211_GGCTAC_S11_R1_merged.fastq.gz
- GSM8226684 MCF7_ChIP_MLL1_steadystate_REP1_220531_TTAGGC_S3_R1_merged.fastq.gz
- GSM8226685 T47D_ChIP_BRPF1_steadystate_REP1_230601_GATCAG_S10_R1_merged.fastq.gz
- GSM8226686 T47D_ChIP_input_steadystate_REP1_220531_ACTTGA_S8_R1_merged.fastq.gz
- GSM8226687 T47D_ChIP_input_steadystate_REP1_230601_CGATGT_S4_R1_merged.fastq.gz
- GSM8226688 T47D_ChIP_KAT6A_steadystate_REP1_230601_GCCAAT_S7_R1_merged.fastq.gz
- GSM8226689 T47D_ChIP_MEN1_steadystate_REP1_220531_GCCAAT_S6_R1_merged.fastq.gz
- GSM8226690 T47D_ChIP_MLL1_steadystate_REP1_220531_CAGATC_S7_R1_merged.fastq.gz
+ 29 more — browse all 69 samples with per-sample file links →
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Share this dataset
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