ChIP analysis of H3K9me3 and H3K4me3 for mouse spermatogonia and leptotene/zygotene spermatocytes defficient in Dnmt3l and Pld6.
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.
- Paper
- DNA methylation dictates histone modifications in developing male germ cells in the mouseNucleic acids research · 2025
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 GSE296269_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 PRJNA1258306 and SRA study SRP582894. 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.
- GSM8967877 ChIP wild-type, P7, H3K4me3 (07-473)
- GSM8967878 ChIP wild-type, P7, H3K9me3 (MABI0308)
- GSM8967879 ChIP wild-type, P7, input
- GSM8967880 ChIP Dnmt3l KO, P7, H3K4me3 (07-473)
- GSM8967881 ChIP Dnmt3l KO, P7, H3K9me3 (MABI0308)
- GSM8967882 ChIP Dnmt3 KO, P7, input
- GSM8967883 ChIP Pld6 KO, P7, H3K4me3 (07-473)
- GSM8967884 ChIP Pld6 KO, P7, H3K9me3 (MABI0308)
- GSM8967885 ChIP Pld6 KO, P7, input
- GSM9034624 ChIP wild-type, P21, H3K4me3 (07-473)
- GSM9034625 ChIP wild-type, P21, H3K9me3 (MABI0308)
- GSM9034626 ChIP wild-type, P21, input
- GSM9034627 ChIP Dnmt3l KO, P21, H3K4me3 (07-473)
- GSM9034628 ChIP Dnmt3l KO, P21, H3K9me3 (MABI0308)
- GSM9034629 ChIP Dnmt3 KO, P21, input
- GSM9034630 ChIP Pld6 KO, P21, H3K4me3 (07-473)
- GSM9034631 ChIP Pld6 KO, P21, H3K9me3 (MABI0308)
- GSM9034632 ChIP Pld6 KO, P21, input
- GSE296268 Retrotransposon expression analysis for mouse spermatogonia defficient in Dnmt3l and Pld6. 19 samples shares dnmt3l, pld6, spermatogonia, defficient
- GSE317929 Effect of intrauterine growth restriction on the H3K4me3, H3K9ac, H3K27ac and H3k9me3 histione modification of microglia in hippocampus 34 samples shares h3k9me3, h3k4me3
- GSE267479 H3K4me3 and H3K9me3 histone modification profiles of uterine stromal cells from young and aged mouse females 18 samples shares h3k9me3, h3k4me3
- GSE231845 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ChIP-Seq] 216 samples shares h3k9me3
- GSE73952 Distinct features in establishing H3K4me3 and H3K27me3 in pre-implantation embryos 67 samples shares h3k4me3
- GSE273948 Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability 56 samples shares h3k9me3
- GSE289600 CFP1-mediated H3K4me3 broad domains control early B cell lineage fate determination [Cut&Tag] 52 samples shares h3k4me3
- GSE190102 Ageing-Related Changes to H3K4me3, H3K27ac and H3K27me3 in Purified Mouse Neurons 43 samples shares h3k4me3
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.