Characterization of the role of SETDB1 in Muscle stem cells during skeletal muscle regeneration
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 × Control_OIL_biol vs 3 × Setdb1_KO_TAM_biolGroups 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 GSE233396_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 PRJNA976186. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 6 samples.
How we read this: 2 replicated groups read from 10 sample titles; they account for 6 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.
- GSM7426788 Control bio rep1 and rep 2 [ATAC-seq]
- GSM7426789 Setdb1-KO bio rep1 and rep 2[ATAC-seq]
- GSM7426790 Control_OIL_biol rep 1 Control_OIL_biol
- GSM7426791 Control_OIL_biol rep 2 Control_OIL_biol
- GSM7426792 Control_OIL_biol rep 3 Control_OIL_biol
- GSM7426793 Setdb1_KO_TAM_biol rep1 Setdb1_KO_TAM_biol
- GSM7426794 Setdb1_KO_TAM_biol rep2 Setdb1_KO_TAM_biol
- GSM7426795 Setdb1_KO_TAM_biol rep3 Setdb1_KO_TAM_biol
- GSM7426796 WT [scRNA-seq]
- GSM7426797 KO [scRNA-seq]
- GSE303540 In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells [sgRNA] 272 samples shares skeletal, muscle, stem
- GSE327391 In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells [control] 81 samples shares skeletal, muscle, stem
- GSE327392 In vivo systematic detection of the outcomes of CRISPR/Cas9 mediated DNA repair in skeletal muscle stem cells [IDM-Seq long-read] 12 samples shares skeletal, muscle, stem
- GSE263619 Hydrogel biomaterials that stiffen and soften on demand reveal that skeletal muscle stem cells harbor a mechanical memory 10 samples shares skeletal, muscle, stem
- GSE250202 Yin Yang 1 Deficiency in Skeletal Muscle Stem Cell Aggravates Muscle Fibrosis in Duchenne Muscular Dystrophy Mouse by Disrupting Muscle Stem Cell/Macrophage/Fibro-adipogenic Progenitor Crosstalk [RNA-Seq] 12 samples shares skeletal, muscle, stem
- GSE306935 The Integrated Stress Response Pathway Improves Aged Murine Muscle Stem Cell Activation and in vivo Regeneration 12 samples shares regeneration, muscle, stem
- GSE329069 Deletion of P311 enhances regeneration in aged skeletal muscle 9 samples shares regeneration, skeletal, muscle
- GSE279796 Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability 18 samples shares setdb1, stem
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.