Setdb1 regulates proper differentiation of adult intestinal stem cells via restraining permissive chromatin structure and transcriptional variability
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 18 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
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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 GSE279796_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 PRJNA1174708 and SRA study SRP539356. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 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.
- GSM8580411 GFP_WT replicate 1, scRNA
- GSM8580412 GFP_WT replicate 2, scRNA
- GSM8580413 GFP_Setdb1KO replicate 1, scRNA
- GSM8580414 GFP_Setdb1KO replicate 2, scRNA
- GSM8580415 GFP_ WT, replicate 1 Total RNA-seq
- GSM8580416 GFP_ WT, replciate 2, Total RNA-seq
- GSM8580417 GFP_ Setdb1KO, replicate 1, Total RNA-seq
- GSM8580418 GFP_Setdb1KO, replicate 2, Total RNA-seq
- GSM8580419 GFP_WT_H3K9me3., replicate 1, ChIP
- GSM8580420 GFP_WT_H3K9me3., replicate 2, ChIP
- GSM8580421 GFP_Setdb1KO_H3K9me3., replicate 1, ChIP
- GSM8580422 GFP_Setdb1KO_Setdb1_H3K9me3., replicate 2, ChIP
- GSM8580423 GFP_WT , scATAC
- GSM8580424 GFP_Setdb1KO, scATAC
- GSM8580425 GFP_ WT nTnG, replicate 1, scRNA
- GSM8580426 GFP_ WT nTnG, replicate 2, scRNA
- GSM8580427 GFP_ Setdb1-KO nTnG, replicate 1, scRNA
- GSM8580428 GFP_ Setdb1-KO nTnG, replicate 2, scRNA
- GSE283662 Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning 22 samples shares intestinal, chromatin
- GSE270622 SETDB1 Orchestrates Metabolic Reprogramming to Regulate Cell State Maintenance and Cell Fate Differentiation 16 samples shares setdb1
- GSE269417 Single embryo total RNA sequencing to map the effect of maternal SETDB1 on the 2-celll and 8-cell transcriptome 37 samples shares setdb1
- GSE247620 Histone methyltransferase SETDB1 silenced SINE B2 retrotransposons and maintained mitotic cell cycle of neural progenitor cells 22 samples shares setdb1
- GSE275353 Exploring the Mechanism of SETDB1 in Regulating Neuroinflammation and Anxiety-Depression-like Behaviors [RNA-seq] 19 samples shares setdb1
- GSE268907 MGA directly recruits SETDB1/ATF7IP for histone H3K9me3 on meiosis-related genes in mouse embryonic stem cells. 12 samples shares setdb1
- GSE318069 eIF4G2-mediated Translation Initiation of Histone Modifiers is Essential for Intestinal Stem Cell Maintenance and Differentiation 145 samples shares intestinal
- GSE288156 Progressive intestinal tumor cell plasticity, Myc activation and loss of Lgr5+ tumor stem cell lineage commitment upon Wnt depletion 14 samples shares intestinal
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.