Changes in histone modifications measured by CUT&RUN after lipid exposure
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 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
- 16 samples: 6 conditions, mostly in triplicateGroups 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
- A metabolic shift to the serine pathway induced by lipids fosters epigenetic reprogramming in nontransformed breast cellsScience advances · 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 GSE283777_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 PRJNA1195569 and SRA study SRP550062. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 6 replicated groups read from 16 sample titles; they account for 16 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.
- GSM8672183 Negative ctrl, replicate 1 Negative ctrl,
- GSM8672184 Negative ctrl, replicate 2 Negative ctrl,
- GSM8672185 Positive ctrl, replicate 1 Positive ctrl,
- GSM8672186 Positive ctrl, replicate 2 Positive ctrl,
- GSM8672187 Vehicle, H3K4me3, replicate 1 Vehicle, H3K4me3,
- GSM8672188 Vehicle, H3K4me3, replicate 2 Vehicle, H3K4me3,
- GSM8672189 Vehicle, H3K4me3, replicate 3 Vehicle, H3K4me3,
- GSM8672190 Octanoic Acid, H3K4me3, replicate 1 Octanoic Acid, H3K4me3,
- GSM8672191 Octanoic Acid, H3K4me3, replicate 2 Octanoic Acid, H3K4me3,
- GSM8672192 Octanoic Acid, H3K4me3, replicate 3 Octanoic Acid, H3K4me3,
- GSM8672193 Vehicle, H3K27me3, replicate 1 Vehicle, H3K27me3,
- GSM8672194 Vehicle, H3K27me3, replicate 2 Vehicle, H3K27me3,
- GSM8672195 Vehicle, H3K27me3, replicate 3 Vehicle, H3K27me3,
- GSM8672196 Octanoic Acid, H3K27me3, replicate 1 Octanoic Acid, H3K27me3,
- GSM8672197 Octanoic Acid, H3K27me3, replicate 2 Octanoic Acid, H3K27me3,
- GSM8672198 Octanoic Acid, H3K27me3, replicate 3 Octanoic Acid, H3K27me3,
- GSE269555 Targeting the oncohistone-ASCL1 axis disrupts plasticity and suppresses pediatric gliomas [CUT&RUN] 39 samples shares cut, run, histone
- GSE303343 A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN] 48 samples shares cut, run
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares cut, run
- GSE278910 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN] 30 samples shares cut, run
- GSE301512 Chromatin topology dynamics of dexamethasone-treated trabecular meshwork identifies 78 causal genes for intraocular pressure and primary open angle glaucoma [CUT&Run] 30 samples shares cut, run
- GSE253893 PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma [Cut&Run] 28 samples shares cut, run
- GSE267470 Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [CUT&RUN] 12 samples shares cut, run
- GSE316989 Targeting CDK12/CYCLIN K induces a gene activation program which is mediated by P-TEFb [Cut&RUN] 10 samples shares cut, run
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.