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Dynamic dysregulation of the transcriptome upon deletion of Mecp2 in adult mice [CUT&RUN]

GSE246664 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 168 samples Submitted 2024/12/16 Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 168 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
168 samples: 56 conditions, mostly in triplicateGroups 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
Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesisNeuron · 2025
Summary (written by the submitters)
Loss of function mutations in methyl Cpg binding protein 2 (MECP2) cause Rett syndrome. Loss of MeCP2 causes global transcriptional dysregulation, but it was unknown whether this transcriptional dysregulation was proximal to Mecp2 function. We deleted Mecp2 from adult mice and performed a time-series CUT&RUN experiment to identify if MeCP2 binding or histone post-translational modficiations are altered immediately upon loss of MeCP2.
Published in
Acute MeCP2 loss in adult mice reveals transcriptional and chromatin changes that precede neurological dysfunction and inform pathogenesis
Bajikar SS, Zhou J, O'Hara R et al. · Neuron 2025 · PMID 39689710 · doi:10.1016/j.neuron.2024.11.006
This dataset
Open GSE246664 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →
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.

Series matrix ↓
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 GSE246664_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
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.

Raw reads on ENA ↗

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 PRJNA1030893 and SRA study SRP467811. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39689710) ↗
Study design
56 conditions, mostly in triplicate
Week1_Vehicle_IgG ×3 Week1_Tamoxifen_aKO_IgG ×3 Week2_Vehicle_IgG ×3 Week2_Tamoxifen_aKO_IgG ×3 Week4_Vehicle_IgG ×3 Week4_Tamoxifen_aKO_IgG ×3 Week8_Vehicle_IgG ×3 Week8_Tamoxifen_aKO_IgG ×3 +48 more

Supports a between-group comparison across 168 samples.

How we read this: 56 replicated groups read from 168 sample titles; they account for 168 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

+ 128 more — browse all 168 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

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.