Persistent open chromatin state in early-life stress-activated cells of the VTA
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: 3 × els, adult, activated, vs 3 × els, adult, non-activated, vs 2 × std, adult, activated, vs 2 × std, adult, non-activated,Groups 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
- Persistent open chromatin state in early-life stress-activated cells of the VTAScientific reports · 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 GSE268468_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 PRJNA1117426 and SRA study SRP510273. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 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.
- GSM9062059 std, adult, activated, replicate 1 std, adult, activated,
- GSM9062060 std, adult, activated, replicate 2 std, adult, activated,
- GSM9062061 els, adult, activated, replicate 1 els, adult, activated,
- GSM9062062 els, adult, activated, replicate 2 els, adult, activated,
- GSM9062063 els, adult, activated, replicate 3 els, adult, activated,
- GSM9062064 std, adult, non-activated, replicate 1 std, adult, non-activat…
- GSM9062065 std, adult, non-activated, replicate 2 std, adult, non-activat…
- GSM9062066 els, adult, non-activated, replicate 1 els, adult, non-activat…
- GSM9062067 els, adult, non-activated, replicate 2 els, adult, non-activat…
- GSM9062068 els, adult, non-activated, replicate 3 els, adult, non-activat…
- GSE324599 Early-life stress alters chromatin modifications in VTA to prime stress sensitivity 13 samples shares vta, early-life, chromatin
- GSE223050 The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1–linked chromatin opening 336 samples shares early-life, chromatin, open
- GSE262927 A longitudinal atlas of post-viral lung regeneration reveals persistent injury-associated cell states 33 samples shares persistent, state
- GSE276171 STAT3S727 Phosphorylation in VTA Dopaminergic Neurons Competed by O-GlcNAcylation Regulates Acute Stress-Induced Anxiety and Reward Inhibition [ATAC-Seq] 6 samples shares vta
- GSE273040 VTA dopamine neurons are hyperexcitable in 3xTg-AD mice due to casein kinase 2-dependent SK channel dysfunction 68 samples shares vta
- GSE276319 The ion channel mechanisms of the subthreshold inward depolarizing currents in the VTA dopaminergic neurons and their roles in the depression-like behavior 45 samples shares vta
- GSE303538 Stress resilience is associated with transcriptional remodeling in the VTA 34 samples shares vta
- GSE342034 Matched short-read and long-read single-nucleus RNA-sequencing of substantia nigra / VTA and olfactory bulb from SNCA-GR humanized-knock-in mice 12 samples shares vta
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.