Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 259 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
- 259 samples: 96 conditions, mostly in duplicateGroups 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.
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 GSE281151_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 PRJNA1182386. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 70 samples read as cases, 61 as controls.
How we read this: 96 replicated groups read from 259 sample titles; they account for 233 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.
- GSM8599120 ATAC-seq mESC DMSO control replicate 1 ATAC-seq mESC DMSO cont…
- GSM8599121 ATAC-seq mESC DMSO control replicate 2 ATAC-seq mESC DMSO cont…
- GSM8599122 ATAC-seq mESC TSA-treated replicate 1 ATAC-seq mESC TSA-treat…
- GSM8599123 ATAC-seq mESC TSA-treated replicate 2 ATAC-seq mESC TSA-treat…
- GSM8599124 ATAC-seq mESC 24h recovery after TSA washout replicate 1 ATAC-seq mESC 24h recov…
- GSM8599125 ATAC-seq mESC 24h recovery after TSA washout replicate 2 ATAC-seq mESC 24h recov…
- GSM8599126 H3K4me1 ChIP-seq of mESC DMSO control rep1 H3K4me1 ChIP-seq of mES…
- GSM8599127 H3K4me1 ChIP-seq of mESC DMSO control rep2 H3K4me1 ChIP-seq of mES…
- GSM8599128 H3K4me1 ChIP-seq of mESC TSA-treated rep1 H3K4me1 ChIP-seq of mES…
- GSM8599129 H3K4me1 ChIP-seq of mESC TSA-treated rep2 H3K4me1 ChIP-seq of mES…
- GSM8599130 H3K4me1 ChIP-seq mESC 24h recovery after TSA washout rep1 H3K4me1 ChIP-seq mESC 2…
- GSM8599131 H3K4me1 ChIP-seq mESC 24h recovery after TSA washout rep2 H3K4me1 ChIP-seq mESC 2…
- GSM8599132 H3K4me3 ChIP-seq of mESC DMSO control rep1 H3K4me3 ChIP-seq of mES…
- GSM8599133 H3K4me3 ChIP-seq of mESC DMSO control rep2 H3K4me3 ChIP-seq of mES…
- GSM8599134 H3K4me3 ChIP-seq of mESC TSA-treated rep1 H3K4me3 ChIP-seq of mES…
- GSM8599135 H3K4me3 ChIP-seq of mESC TSA-treated rep2 H3K4me3 ChIP-seq of mES…
- GSM8599136 H3K4me3 ChIP-seq mESC 24h recovery after TSA washout rep1 H3K4me3 ChIP-seq mESC 2…
- GSM8599137 H3K4me3 ChIP-seq mESC 24h recovery after TSA washout rep2 H3K4me3 ChIP-seq mESC 2…
- GSM8599138 H3K9me3 ChIP-seq of mESC DMSO control rep1 H3K9me3 ChIP-seq of mES…
- GSM8599139 H3K9me3 ChIP-seq of mESC DMSO control rep2 H3K9me3 ChIP-seq of mES…
- GSM8599140 H3K9me3 ChIP-seq of mESC TSA-treated rep1 H3K9me3 ChIP-seq of mES…
- GSM8599141 H3K9me3 ChIP-seq of mESC TSA-treated rep2 H3K9me3 ChIP-seq of mES…
- GSM8599142 H3K9me3 ChIP-seq mESC 24h recovery after TSA washout rep1 H3K9me3 ChIP-seq mESC 2…
- GSM8599143 H3K9me3 ChIP-seq mESC 24h recovery after TSA washout rep2 H3K9me3 ChIP-seq mESC 2…
- GSM8599144 H3K27me3 ChIP-seq of mESC DMSO control rep1 H3K27me3 ChIP-seq of mE…
- GSM8599145 H3K27me3 ChIP-seq of mESC DMSO control rep2 H3K27me3 ChIP-seq of mE…
- GSM8599146 H3K27me3 ChIP-seq of mESC TSA-treated rep1 H3K27me3 ChIP-seq of mE…
- GSM8599147 H3K27me3 ChIP-seq of mESC TSA-treated rep2 H3K27me3 ChIP-seq of mE…
- GSM8599148 H3K27me3 ChIP-seq mESC 24h recovery after TSA washout rep1 H3K27me3 ChIP-seq mESC …
- GSM8599149 H3K27me3 ChIP-seq mESC 24h recovery after TSA washout rep2 H3K27me3 ChIP-seq mESC …
- GSM8599150 H3K27ac ChIP-seq of mESC DMSO control rep1 H3K27ac ChIP-seq of mES…
- GSM8599151 H3K27ac ChIP-seq of mESC DMSO control rep2 H3K27ac ChIP-seq of mES…
- GSM8599152 H3K27ac ChIP-seq of mESC TSA-treated rep1 H3K27ac ChIP-seq of mES…
- GSM8599153 H3K27ac ChIP-seq of mESC TSA-treated rep2 H3K27ac ChIP-seq of mES…
- GSM8599154 H3K27ac ChIP-seq mESC 24h recovery after TSA washout rep1 H3K27ac ChIP-seq mESC 2…
- GSM8599155 H3K27ac ChIP-seq mESC 24h recovery after TSA washout rep2 H3K27ac ChIP-seq mESC 2…
- GSM8599156 H2AK119Ub ChIP-seq of mESC DMSO control rep1 H2AK119Ub ChIP-seq of m…
- GSM8599157 H2AK119Ub ChIP-seq of mESC DMSO control rep2 H2AK119Ub ChIP-seq of m…
- GSM8599158 H2AK119Ub ChIP-seq of mESC TSA-treated rep1 H2AK119Ub ChIP-seq of m…
- GSM8599159 H2AK119Ub ChIP-seq of mESC TSA-treated rep2 H2AK119Ub ChIP-seq of m…
+ 219 more — browse all 259 samples with per-sample file links →
- GSE313112 Inhibition of METTL3 by STC-15 induces RNA misprocessing that results in dsRNA formation and activates innate immunity [RNA-Seq MC38] 69 samples shares inhibition, induces
- GSE309517 Inhibition of the cancer stem cell immune checkpoint SOAT1 suppresses regulatory T cell functions through a trans-cellular 20(S)-Hydroxycholesterol-GPR132 pathway in mice. 45 samples shares inhibition, cellular
- GSE266686 Mutant IDH1 inhibition induces dsDNA sensing to activate tumor immunity [ChIP-Seq] 32 samples shares inhibition, induces
- GSE301496 Transient YAP/TAZ inhibition exposes therapeutic vulnerabilities in advanced cancers [CUT&Run] 20 samples shares inhibition, transient
- GSE269433 Histone Deacetylase 1 (HDAC1) maintains the transcriptome of embryonic stem cells through regulating acetylation at crucial genomic sites [ChIP-seq] 18 samples shares deacetylase, histone
- GSE296365 Prenatal stress induces transient developmental alterations in distinct GABAergic populations and leads to long-lasting behavioral abnormalities 16 samples shares transient, induces
- GSE318028 Pharmacological inhibition of FKBP51 mitigates early life adversity-induced social deficits 246 samples shares inhibition
- GSE293819 Monitoring systemic immune responses to checkpoint inhibition in breast cancer reveals host responses and mechanisms of resistance 142 samples shares inhibition
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.