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Dnmt3a1 regulates memory formation via the downstram target Nrp1

GSE232630 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/05/06 Platform GPL23479
At a glance

RNA-seq (gene expression) · mouse · 16 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Mus musculus (mouse)
Samples
16 samples: 4 × hippocampal cultures, shDnmt3a1, 4h Bicuculline, vs 4 × hippocampal cultures, shDnmt3a1, 0h Bicuculline, vs 4 × hippocampal cultures, shControl, 4h Bicuculline, vs 4 × hippocampal cultures, shControl, 0h Bicuculline,Groups 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
Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2024
Summary (written by the submitters)
Epigenetic factors are well established players in memory formation. Specifically, DNA methylation is necessary for the formation of long-term memory in multiple brain regions including the hippocampus. Despite the demonstrated role for DNA methyltransferases (Dnmts) in memory formation whether individual Dnmts play unique or redundant functions in long-term memory formation is not well established.
Read the full summary ↓
Furthermore, the downstream processes controlled by the Dnmts during the consolidation of memory are not investigated. In this study, we investigated the requirement for Dnmt3a1, the predominant Dnmt in the adult brain, in hippocampal long-term memory formation. Furthermore, we identified an activity-regulated Dnmt3a1-dependent genomic program. Our data showed that Dnmt3a1, similarly to its isoform Dnmt3a2, plays a critical role in memory formation. Furthermore, we uncovered Neuropilin 1 (Nrp1) as a downstream target of Dnmt3a1 during the formation of memory. Intriguingly, we found that Nrp1 expression is selectively regulated and a specific downstream effector of Dnmt3a1, but not Dnmt3a2. Taken together, our study uncovered a Dnmt3a isoform specific mechanism in memory formation and further highlighted the complex and highly regulated functions of distinct epigenetic regulators in brain function.
Published in
Dnmt3a1 regulates hippocampus-dependent memory via the downstream target Nrp1
Kupke J, Klimmt J, Mudlaff F et al. · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2024 · PMID 38499720 · doi:10.1038/s41386-024-01843-0
This dataset
Open GSE232630 in finder → Find more mouse RNA-seq 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 GSE232630_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA973052 and SRA study SRP438045. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38499720) ↗
Study design
4 × hippocampal cultures, shDnmt3a1, 4h Bicuculline, vs 4 × hippocampal cultures, shDnmt3a1, 0h Bicuculline, vs 4 × hippocampal cultures, shControl, 4h Bicuculline, vs 4 × hippocampal cultures, shControl, 0h Bicuculline,

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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
Datasets on a similar topic

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