High-dimensional analysis reveals increased chromatin heterogeneity and reduced histone acetylation driven by mutant-IDH1 [Cut&Run]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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
- 10 samples: 10 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
- Oncogenic IDH1(mut) drives robust loss of histone acetylation and increases chromatin heterogeneityProceedings 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 GSE238104_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 PRJNA997972 and SRA study SRP451129. 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 10 sample titles: 10 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.
- GSM7658533 Cut&Run on IHA-noDox using H3K9ac antibody
- GSM7658534 Cut&Run on IHA-noDox using H3K27ac antibody
- GSM7658535 Cut&Run on IHA-noDox using H4K16ac antibody
- GSM7658536 Cut&Run on IHA-noDox using IgG control antibody (2nd HRP)
- GSM7658537 Cut&Run on IHA-2d-Dox using H3K9ac antibody
- GSM7658538 Cut&Run on IHA-2d-Dox using H3K27ac antibody
- GSM7658539 Cut&Run on IHA-2d-Dox using H4K16ac antibody
- GSM7658540 Cut&Run on IHA-7d-Dox using H3K9ac antibody
- GSM7658541 Cut&Run on IHA-7d-Dox using H3K27ac antibody
- GSM7658542 Cut&Run on IHA-7d-Dox using H4K16ac antibody
- GSE301553 The impact of Fulvestrant on Estrogen Receptor-Driven Chromatin Dynamics in breast cancer cells points to a disconnect between chromatin opening and histone acetylation [CUT&Tag] 18 samples shares acetylation, chromatin, histone
- GSE220870 METTL3 Promotes Histone H3K9 Acetylation through Recruitment of Histone Acetyltransferase 1 to Chromatin 43 samples shares acetylation, chromatin, histone
- GSE277183 RNA Polymerase II coordinates histone deacetylation at active promoters 158 samples shares acetylation, histone
- GSE326102 Genome-wide histone acetylation underscores tumor intrinsic immune signaling induced by photothermal therapy in ovarian cancer 56 samples shares acetylation, histone
- GSE307716 Small interfering RNA-mediated silencing of mutant NPM1 suppresses acute myeloid leukemia via reversing KAT7 and p300-mediated histone acetylation [CUT&Tag] 52 samples shares acetylation, histone
- GSE286492 CUT&Tag recovers up to half of ENCODE ChIP-seq histone acetylation peaks 38 samples shares acetylation, histone
- GSE280616 H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment [CUT&Tag] 16 samples shares heterogeneity, chromatin
- GSE280618 H3K27me3 chromatin heterogeneity reveals variable cell responses to estrogen and endocrine treatment 34 samples shares heterogeneity, chromatin
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.