GEO series
Duplication of autism-related gene Chd8 leads to behavioral hyperactivity and neurodevelopmental defects in mice
GSE263334
Mus musculus (mouse)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
40 samples
Submitted 2025/04/05
Platform GPL24247
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 40 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
- 40 samples: 10 conditions, mostly with about 5 replicates eachGroups 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
- Duplication of the autism-related gene Chd8 leads to behavioral hyperactivity and neurodevelopmental defects in miceNature communications · 2025
Summary (written by the submitters)
Mutations in the gene encoding the chromodomain helicase DNA-binding protein 8 (CHD8) are strongly associated with autism spectrum disorder (ASD). Although duplications of the locus spanning CHD8 are also found in individuals with neurodevelopmental disorders, the role of CHD8 duplication in clinical phenotypes and the underlying mechanisms have remained unknown.
Read the full summary ↓
Here we show that mice with Chd8 overexpression modeling human CHD8 duplication manifest growth retardation, microcephaly, and behavioral abnormalities including hyperactivity and reduced anxiety-like behavior. Chd8 overexpression results in alterations of transcription and chromatin accessibility of genes involved in neurogenesis that are associated with aberrant binding of CHD8 to enhancer regions and impairs differentiation of deep-layer neurons. Furthermore, genetic and pharmacological interventions rescue hyperactive behavior of Chd8 overexpression mice. Our results thus indicate that Chd8 overexpression mice recapitulate key features of CHD8 duplication syndrome, and they provide insight into cellular and molecular pathogenesis underlying neurodevelopmental disorders.
Published in
Kawamura A, Fujii K, Tamada K et al.
· Nature communications 2025
· PMID 40419468
· doi:10.1038/s41467-025-59853-5
This dataset
Download · which file do I need?
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.
1 · Just have a look
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.
2 · Re-analyse it
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE263334_RAW.tar (it can run to tens of gigabytes).
3 · Start from the raw reads
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 PRJNA1096729 and SRA study SRP500009. Searching any of these in the dataset finder brings you back here.
Study design
10 conditions, mostly with about 5 replicates each
RNA-seq E14 forebrain CHD8 WT ×5
RNA-seq E14 forebrain CHD8 KI ×5
RNA-seq E18 forebrain CHD8 WT ×5
RNA-seq E18 forebrain CHD8 KI ×5
ATAC-seq E14 forebrain CHD8 WT ×4
ATAC-seq E14 forebrain CHD8 KI ×4
ChIP-seq input E14 forebrain CHD8 WT ×3
ChIP-seq CHD8 E14 forebrain CHD8 WT ×3
+2 more
Supports a between-group comparison across 40 samples.
How we read this: 10 replicated groups read from 40 sample titles; they account for 40 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.
Samples in this study
- GSM8189713 RNA-seq E14 forebrain CHD8 WT rep1 RNA-seq E14 forebrain C…
- GSM8189714 RNA-seq E14 forebrain CHD8 WT rep2 RNA-seq E14 forebrain C…
- GSM8189715 RNA-seq E14 forebrain CHD8 WT rep3 RNA-seq E14 forebrain C…
- GSM8189716 RNA-seq E14 forebrain CHD8 WT rep4 RNA-seq E14 forebrain C…
- GSM8189717 RNA-seq E14 forebrain CHD8 WT rep5 RNA-seq E14 forebrain C…
- GSM8189718 RNA-seq E14 forebrain CHD8 KI rep1 RNA-seq E14 forebrain C…
- GSM8189719 RNA-seq E14 forebrain CHD8 KI rep2 RNA-seq E14 forebrain C…
- GSM8189720 RNA-seq E14 forebrain CHD8 KI rep3 RNA-seq E14 forebrain C…
- GSM8189721 RNA-seq E14 forebrain CHD8 KI rep4 RNA-seq E14 forebrain C…
- GSM8189722 RNA-seq E14 forebrain CHD8 KI rep5 RNA-seq E14 forebrain C…
- GSM8189723 RNA-seq E18 forebrain CHD8 WT rep1 RNA-seq E18 forebrain C…
- GSM8189724 RNA-seq E18 forebrain CHD8 WT rep2 RNA-seq E18 forebrain C…
- GSM8189725 RNA-seq E18 forebrain CHD8 WT rep3 RNA-seq E18 forebrain C…
- GSM8189726 RNA-seq E18 forebrain CHD8 WT rep4 RNA-seq E18 forebrain C…
- GSM8189727 RNA-seq E18 forebrain CHD8 WT rep5 RNA-seq E18 forebrain C…
- GSM8189728 RNA-seq E18 forebrain CHD8 KI rep1 RNA-seq E18 forebrain C…
- GSM8189729 RNA-seq E18 forebrain CHD8 KI rep2 RNA-seq E18 forebrain C…
- GSM8189730 RNA-seq E18 forebrain CHD8 KI rep3 RNA-seq E18 forebrain C…
- GSM8189731 RNA-seq E18 forebrain CHD8 KI rep4 RNA-seq E18 forebrain C…
- GSM8189732 RNA-seq E18 forebrain CHD8 KI rep5 RNA-seq E18 forebrain C…
- GSM8189733 ChIP-seq input E14 forebrain CHD8 WT rep1 ChIP-seq input E14 fore…
- GSM8189734 ChIP-seq input E14 forebrain CHD8 WT rep2 ChIP-seq input E14 fore…
- GSM8189735 ChIP-seq input E14 forebrain CHD8 WT rep3 ChIP-seq input E14 fore…
- GSM8189736 ChIP-seq CHD8 E14 forebrain CHD8 WT rep1 ChIP-seq CHD8 E14 foreb…
- GSM8189737 ChIP-seq CHD8 E14 forebrain CHD8 WT rep2 ChIP-seq CHD8 E14 foreb…
- GSM8189738 ChIP-seq CHD8 E14 forebrain CHD8 WT rep3 ChIP-seq CHD8 E14 foreb…
- GSM8189739 ChIP-seq input E14 forebrain CHD8 KI rep1 ChIP-seq input E14 fore…
- GSM8189740 ChIP-seq input E14 forebrain CHD8 KI rep2 ChIP-seq input E14 fore…
- GSM8189741 ChIP-seq input E14 forebrain CHD8 KI rep3 ChIP-seq input E14 fore…
- GSM8189742 ChIP-seq CHD8 E14 forebrain CHD8 KI rep1 ChIP-seq CHD8 E14 foreb…
- GSM8189743 ChIP-seq CHD8 E14 forebrain CHD8 KI rep2 ChIP-seq CHD8 E14 foreb…
- GSM8189744 ChIP-seq CHD8 E14 forebrain CHD8 KI rep3 ChIP-seq CHD8 E14 foreb…
- GSM8189745 ATAC-seq E14 forebrain CHD8 WT rep1 ATAC-seq E14 forebrain …
- GSM8189746 ATAC-seq E14 forebrain CHD8 WT rep2 ATAC-seq E14 forebrain …
- GSM8189747 ATAC-seq E14 forebrain CHD8 WT rep3 ATAC-seq E14 forebrain …
- GSM8189748 ATAC-seq E14 forebrain CHD8 WT rep4 ATAC-seq E14 forebrain …
- GSM8189749 ATAC-seq E14 forebrain CHD8 KI rep1 ATAC-seq E14 forebrain …
- GSM8189750 ATAC-seq E14 forebrain CHD8 KI rep2 ATAC-seq E14 forebrain …
- GSM8189751 ATAC-seq E14 forebrain CHD8 KI rep3 ATAC-seq E14 forebrain …
- GSM8189752 ATAC-seq E14 forebrain CHD8 KI rep4 ATAC-seq E14 forebrain …
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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.