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Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration

GSE226580 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 94 samples Submitted 2024/10/17 Platform GPL34290Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 94 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
94 samples: 35 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.
Paper
Stem cell activity-coupled suppression of endogenous retrovirus governs adult tissue regenerationCell · 2024
Summary (written by the submitters)
Mammalian retrotransposons constitute 40% of the genome. During tissue regeneration, adult stem cells coordinately repress retrotransposons and activate lineage genes, but how this coordination is controlled is poorly understood. Here, we observed that dynamic expression of histone methyltransferase SETDB1 (a retrotransposon repressor) closely mirrors stem cell activities in the murine skin.
Read the full summary ↓
SETDB1 ablation leads to reactivation of endogenous retroviruses (ERVs, a type of retrotransposon) and assembly of viral-like particles, resulting in hair loss and stem cell exhaustion that is reversible by antiviral drugs. Mechanistically, at least two molecularly and spatially distinct pathways are responsible: antiviral defense mediated by hair follicle stem cells and progenitors, and antiviral independent response due to replication stress in transient amplifying cells. ERV reactivation is promoted by DNA demethylase TET-mediated hydroxymethylation and recapitulated by ablating cell fate transcription factors. Together, we demonstrated ERV silencing is coupled with stem cell activity and essential for adult hair regeneration.
Published in
Stem cell activity-coupled suppression of endogenous retrovirus governs adult tissue regeneration
Lyu Y, Kim SJ, Humphrey ES et al. · Cell 2024 · PMID 39476839 · doi:10.1016/j.cell.2024.10.007
This dataset
Open GSE226580 in finder → Find more mouse RNA-seq datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE226580_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA940720 and SRA study SRP425525. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39476839) ↗
Study design
35 conditions, mostly in duplicate
Ana_HF_Setdb1_cKO ×4 Dnmt1_Het ×4 Dnmt1_cKO ×4 Tlr3-/-_Setdb1_cKO ×4 Ana_HF_Setdb1_Het ×3 ATAC_Ana_HF_Setdb1_Het ×2 ATAC_Ana_HF_Setdb1_cKO ×2 ChIP_Ana_HF_Het_H3K9me3 ×2 +42 more

Supports a between-group comparison across 79 samples.

How we read this: 35 replicated groups read from 94 sample titles; they account for 79 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.

Samples in this study

+ 54 more — browse all 94 samples with per-sample file links →

Datasets on a similar topic

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