Mapping H3K9me3 enrichment upon heterochromatin induction in early embryos.
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: 4 × H3K9me3_mGFP_Control_2C vs 3 × H3K9me3_Suv39h1_2C vs 3 × H3K9me3_PoolJ_2C vs 2 × H3K9me3_GFP_Control_2CGroups 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
- The establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathwaysCell · 2025
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 GSE278718_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 PRJNA1168518 and SRA study SRP536454. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8553440 H3K9me3_GFP_Control_2C_rep1 H3K9me3_GFP_Control_2C
- GSM8553441 H3K9me3_GFP_Control_2C_rep2 H3K9me3_GFP_Control_2C
- GSM8553442 H3K9me3_Suv39h1_2C_rep1 H3K9me3_Suv39h1_2C
- GSM8553443 H3K9me3_Suv39h1_2C_rep2 H3K9me3_Suv39h1_2C
- GSM8553444 H3K9me3_Suv39h1_2C_rep3 H3K9me3_Suv39h1_2C
- GSM8553445 H3K9me3_mGFP_Control_2C_rep1 H3K9me3_mGFP_Control_2C
- GSM8553446 H3K9me3_mGFP_Control_2C_rep2 H3K9me3_mGFP_Control_2C
- GSM8553447 H3K9me3_mGFP_Control_2C_rep3 H3K9me3_mGFP_Control_2C
- GSM8553448 H3K9me3_mGFP_Control_2C_rep4 H3K9me3_mGFP_Control_2C
- GSM8553449 H3K9me3_PoolJ_2C_rep1 H3K9me3_PoolJ_2C
- GSM8553450 H3K9me3_PoolJ_2C_rep2 H3K9me3_PoolJ_2C
- GSM8553451 H3K9me3_PoolJ_2C_rep3 H3K9me3_PoolJ_2C
- GSE264193 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [ChIP-seq] 57 samples shares heterochromatin, embryos, early
- GSE263441 H3K27 dimethylation dynamics reveal stepwise establishment of facultative heterochromatin in early mouse embryos [RNA-Seq] 10 samples shares heterochromatin, embryos, early
- GSE231845 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ChIP-Seq] 216 samples shares h3k9me3, heterochromatin
- GSE273948 Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability 56 samples shares h3k9me3, heterochromatin
- GSE233039 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ATAC-Seq] 18 samples shares h3k9me3, heterochromatin
- GSE270213 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [H4K20me3 ChIP-seq] 12 samples shares h3k9me3, heterochromatin
- GSE233040 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [TT-Seq] 30 samples shares h3k9me3, heterochromatin
- GSE165460 Induction of senescence upon loss of the Ash2l subunit of histone H3K4 methyltransferase complexes (ChIP-Seq) 20 samples shares induction, upon
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.