ChIP-seq of histone marks of DP thymocytes from Suv39h1 and Suv39h2 double knockout chimeric mice
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
- 12 samples: 12 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.
- Paper
- Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcriptionGenome research · 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 GSE256245_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 PRJNA1078778 and SRA study SRP490718. 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 12 sample titles: 12 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.
- GSM8091851 CON H3K4me3 replicate
- GSM8091852 CON H3K27ac replicate
- GSM8091853 CON H3K27me3 replicate
- GSM8091854 CON whole cell extract replicate
- GSM8091855 CON IgG replicate
- GSM8091856 DKO H3K4me3 replicate
- GSM8091857 DKO H3K27ac replicate
- GSM8091858 DKO H3K27me3 replicate
- GSM8091859 DKO whole cell extract replicate
- GSM8091860 DKO IgG replicate
- GSM8091861 CON H3K9me3 replicate
- GSM8091862 CON H3K9me3 whole cell extract
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- GSE291272 The placentalia specific histone H3.4 promotes germ cell development and reproductive fitness [ChIP-seq] 41 samples shares chip-seq, histone
- GSE310474 Cell autonomous regional differences in oligodendrocyte precursor cell development and response to oncohistone H3.3 K27M [ChIP-Seq] 40 samples shares chip-seq, histone
- GSE275130 Mediator Subunit MED4 Enforces Metastatic Dormancy in Breast Cancer (Histone ChIP-seq_shMed4) 36 samples shares chip-seq, histone
- GSE196745 Changes in Ikaros binding and histone-modifications upon oncogenic β-catenin activation [ChIP-Seq] 30 samples shares chip-seq, histone
- GSE270581 Chromatin distribution alterations of histone modifacations and PRC2 complex caused by Rack7 deletion in primary astrocyte [ChIP-Seq] 24 samples shares chip-seq, histone
- GSE267320 Early-life ketone body signaling promotes beige fat biogenesis through changes in histone acetylome and β-hydroxybutyrylome [ChIP-seq] 20 samples shares chip-seq, histone
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.