Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [ChIP-seq/hMeDIP]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 25 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
- 25 samples: 19 distinct titles, 6 of them repeatedGroups 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
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 GSE226578_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 PRJNA940722 and SRA study SRP425525. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 25 sample titles: 19 distinct titles with little repetition. 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.
- GSM7079764 ChIP_MIK_IgG_Ctrl
- GSM7079765 ChIP_MIK_Setdb1
- GSM7079766 ChIP_Ana_HF_Setdb1
- GSM7079767 ChIP_Ana_HF_Het_H3K9me3_rep1
- GSM7079768 ChIP_Ana_HF_Het_H3K9me3_rep2
- GSM7079769 ChIP_Ana_HF_KO_H3K9me3_rep1
- GSM7079770 ChIP_Ana_HF_KO_H3K9me3_rep2
- GSM8405736 ChIP_P0_WT_H3K9me3
- GSM8405737 ChIP_P0_Dnmt1cKO_H3K9me3
- GSM8405738 hMedIP_Ana_HF_Setdb1Het_hMeDIP_rep1
- GSM8405739 hMedIP_Ana_HF_Setdb1Het_hMeDIP_rep1_input
- GSM8405740 hMedIP_Ana_HF_Setdb1Het_hMeDIP_rep2
- GSM8405741 hMedIP_Ana_HF_Setdb1Het_hMeDIP_rep2_input
- GSM8405742 hMedIP_Ana_HF_Setdb1cKO_hMeDIP_rep1
- GSM8405743 hMedIP_Ana_HF_Setdb1cKO_hMeDIP_rep1_input
- GSM8405744 hMedIP_Ana_HF_Setdb1cKO_hMeDIP_rep2
- GSM8405745 hMedIP_Ana_HF_Setdb1cKO_hMeDIP_rep2_input
- GSM8405746 hMedIP_P0_WT_hMeDIP_rep1
- GSM8405747 hMedIP_P0_WT_hMeDIP_rep1_input
- GSM8405748 hMedIP_P0_WT_hMeDIP_rep2
- GSM8405749 hMedIP_P0_WT_hMeDIP_rep2_input
- GSM8405750 hMedIP_P0_Dnmt1cKO_hMeDIP_rep1
- GSM8405751 hMedIP_P0_Dnmt1cKO_hMeDIP_rep1_input
- GSM8405752 hMedIP_P0_Dnmt1cKO_hMeDIP_rep2
- GSM8405753 hMedIP_P0_Dnmt1cKO_hMeDIP_rep2_input
- GSE226580 Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration 94 samples shares activity-coupled, regeneration, suppression, endogenous, retrovirus, governs
- GSE226579 Stem Cell Activity-Coupled Suppression of Endogenous Retrovirus Governs Adult Tissue Regeneration [RNA-seq] 47 samples shares activity-coupled, regeneration, suppression, endogenous, retrovirus, governs
- GSE262919 EZH2 deletion does not impact acinar cell regeneration but restricts progression to pancreatic cancer in mice [ChIP-seq] 36 samples shares regeneration, chip-seq
- GSE306920 Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation [CUT&Tag] 22 samples shares endogenous, retrovirus
- GSE306921 Newly Evolved Endogenous Retroviruses Prime the Ovarian Reserve for Activation [RNA-seq] 12 samples shares endogenous, retrovirus
- GSE249591 Gene suppression by PRC2 enhances the gene inductions by Aire and the development of mimetic cell populations 572 samples shares suppression
- GSE267938 Functional optic tract rewiring via subtype- and target-specific axonal regeneration and presynaptic activity enhancement 256 samples shares regeneration
- GSE281035 PAR3-mediated coordination of hepatocyte proliferation, maturation, and architecture in liver development and regeneration 128 samples shares regeneration
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.