GEO series

Sequential transcriptional gates in the thalamo-cortical circuit support memory stabilization [ChIP-seq]

GSE304099 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 13 samples Submitted 2025/09/28 Platform GPL24247

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 13 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: 13 samples: 2 × ChIP_H3K4me3_Ash1lKO_R20 vs 2 × ChIP_H3K4me3_Ash1lKO_R8 vs 2 × ChIP_H3K4me3_CTL_R20 vs 2 × ChIP_H3K4me3_CTL_R8Groups 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: Thalamocortical transcriptional gates coordinate memory stabilizationNature · 2026

Summary (written by the submitters)

The molecular mechanisms that enable memories to persist over long time-scales from days to weeks and months are still poorly understood. To develop insights, we created a behavioral task where by varying the frequency of learned associations, mice formed multiple memories, but only consolidated some while forgetting others, over the span of weeks.

Read the full summary ↓

We then monitored circuit-specific molecular programs that diverge between consolidated and forgotten memories. We identified multiple distinct waves of transcription, i.e., cellular macrostates, specifically in the thalamo-cortical circuit, that defined memory persistence. Notably, a small set of transcriptional regulators appeared sufficient to orchestrate broad molecular programs that enabled entry into these macrostates. Targeted CRISPR-manipulations of these transcriptional regulators revealed that while they had no effects on memory formation, they had prominent, causal, and strikingly time-dependent roles in memory stabilization. In particular, the calmodulin-dependent transcription factor Camta1 was required for initial memory maintenance over days, while Tcf4 and the histone methyl-transferase Ash1L were required later to maintain memory over weeks. These results identify a critical Camta1-Tcf4-Ash1L thalamo-cortical transcriptional cascade required for memory stabilization, and puts forth a model where the sequential, multi-step, recruitment of circuit-specific transcriptional programs enable memory maintenance over progressively longer time-scales.

Published in

Thalamocortical transcriptional gates coordinate memory stabilization

Terceros A, Chen C, Harada Y et al. · Nature 2026 · PMID 41299170 · doi:10.1038/s41586-025-09774-6

This dataset

Open GSE304099 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 GSE304099_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 PRJNA1298908 and SRA study SRP604703. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41299170) ↗

Study design

2 × ChIP_H3K4me3_Ash1lKO_R20 vs 2 × ChIP_H3K4me3_Ash1lKO_R8 vs 2 × ChIP_H3K4me3_CTL_R20 vs 2 × ChIP_H3K4me3_CTL_R8

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 13 sample titles; they account for 8 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

GSM9143387 ChIP_CAMTA1_Milli_CTL_R8_rep1
GSM9143388 ChIP_CAMTA1_Milli_Camta1KO_R8_rep1
GSM9143389 ChIP_H3K4me3_Ash1lKO_R20_rep1 ChIP_H3K4me3_Ash1lKO_R20
GSM9143390 ChIP_H3K4me3_Ash1lKO_R20_rep2 ChIP_H3K4me3_Ash1lKO_R20
GSM9143391 ChIP_H3K4me3_Ash1lKO_R8_rep1 ChIP_H3K4me3_Ash1lKO_R8
GSM9143392 ChIP_H3K4me3_Ash1lKO_R8_rep2 ChIP_H3K4me3_Ash1lKO_R8
GSM9143393 ChIP_H3K4me3_CTL_R20_rep1 ChIP_H3K4me3_CTL_R20
GSM9143394 ChIP_H3K4me3_CTL_R20_rep2 ChIP_H3K4me3_CTL_R20
GSM9143395 ChIP_H3K4me3_CTL_R8_rep1 ChIP_H3K4me3_CTL_R8
GSM9143396 ChIP_H3K4me3_CTL_R8_rep2 ChIP_H3K4me3_CTL_R8
GSM9143397 ChIP_Input_CTL_R8_rep1
GSM9143398 ChIP_TCF4_Abcam_CTL_R8_rep1
GSM9143399 ChIP_TCF4_Abcam_TCF4KO_R8_rep1

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