A histone hyperacetylation pulse induces cellular memory of gene expression and 3-dimensional genome folding [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 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
- Mus musculus (mouse)
- Samples
- 10 samples: 5 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.
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 GSE280486_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 PRJNA1117356 and SRA study SRP510225. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 2 samples read as cases, 2 as controls.
How we read this: 5 replicated groups read from 10 sample titles; they account for 10 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…
- GSM9097189 ATAC-seq mESC after second TSA pulse rep1 ATAC-seq mESC after sec…
- GSM9097190 ATAC-seq mESC after second TSA pulse rep2 ATAC-seq mESC after sec…
- GSM9097191 ATAC-seq mESC after second 24h recovery rep1 ATAC-seq mESC after sec…
- GSM9097192 ATAC-seq mESC after second 24h recovery rep2 ATAC-seq mESC after sec…
- GSE281151 Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding 259 samples shares cellular, histone, induces, folding, memory
- GSE271884 GFI1-driven transcriptional and epigenetic programs maintain memory CD8+ T cell persistence [ATAC-seq]. 30 samples shares atac-seq, memory
- GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares atac-seq, memory
- GSE236575 Adipose tissue retains an epigenetic memory of obesity after weight loss [ATAC-seq] 22 samples shares atac-seq, memory
- GSE254919 Extracellular vesicles from obese visceral adipose promote pancreatic cancer development and resistance to immune checkpoint blockade therapy [ATAC-seq] 12 samples shares cellular, atac-seq
- GSE246213 A Mouse Model for Metabolic Dysfunction-associated Steatotic Liver Disease and Hepatocellular Carcinoma [ATAC-seq] 12 samples shares cellular, atac-seq
- GSE306916 Efferocytosis induces proangiogenic function and chromatin remodeling in tumor-associated macrophages [ATAC-seq] 12 samples shares atac-seq, induces
- GSE299995 Transcriptional control of Sulf1 by WT1 primes epicardial signalling and fate by modifying extracellular heparan sulfate status [ATAC-Seq] 4 samples shares cellular, atac-seq
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.