GEO series
Neuronal Activity Suppresses NEUROD-Dependent Transcription and Genome Organization [RNA-Seq]
GSE310753
Mus musculus (mouse)
RNA-seq (gene expression)
73 samples
Submitted 2026/01/09
Platform GPL21626
At a glance
RNA-seq (gene expression) · mouse · 73 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
- 73 samples: 13 conditions, mostly with about 4 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
- Neuronal Activity Suppresses NEUROD-Dependent Transcription and Genome OrganizationThe Journal of neuroscience : the official journal of the Society for Neuroscience · 2026
Summary (written by the submitters)
Neuronal activity induces gene expression programs associated with plasticity in the brain, but it also transiently suppresses gene expression through poorly understood mechanisms. Here, we report that neuronal activity downregulates NEUROD-dependent gene expression in cerebellar granule neurons in adult mice. Using NEUROD1/2 double conditional knockout mice of both sexes, we show that NEUROD binds and activates its target gene enhancers and establishes a three-dimensional genome architecture that facilitates transcription when neuronal activity is low.
Read the full summary ↓
Moreover, NEUROD antagonizes activity-dependent gene expression programs, including those regulated by MEF2. However, when granule neurons are activated, NEUROD-dependent transcriptional and genome organizing functions are disrupted. Together, these findings reveal NEUROD as a key regulator of transcriptional programs associated with inactive neurons. Our study provides new insights into how neuronal activity reshapes gene transcription and genome architecture in the brain.
Published in
Valnegri P, Yamada T, Yang Y
· The Journal of neuroscience : the official journal of the Society for Neuroscience 2026
· PMID 41513463
· doi:10.1523/JNEUROSCI.1565-25.2025
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 GSE310753_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: 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 PRJNA1367027 and SRA study SRP648324. Searching any of these in the dataset finder brings you back here.
Study design
13 conditions, mostly with about 4 replicates each
RNA-seq ADCV, chromatin fraction, Adult homec… ×27
RNA-seq ADCV, chromatin fraction, Adult 30m o… ×5
RNA-seq ADCV, Adult ctrl, ×4
RNA-seq ADCV, Adult nd1 cKO, ×4
RNA-seq ADCV, Adult nd2 cKO, ×4
RNA-seq ADCV, Adult nd1/2 dcKO, ×4
RNA-seq ADCV, chromatin fraction, Adult 10m o… ×4
RNA-seq ADCV, chromatin fraction, Adult 30m o… ×4
+5 more
Supports a between-group comparison across 73 samples.
How we read this: 13 replicated groups read from 73 sample titles; they account for 73 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
- GSM9307962 RNA-seq ADCV, Adult ctrl, rep1 RNA-seq ADCV, Adult ctr…
- GSM9307963 RNA-seq ADCV, Adult ctrl, rep2 RNA-seq ADCV, Adult ctr…
- GSM9307964 RNA-seq ADCV, Adult ctrl, rep3 RNA-seq ADCV, Adult ctr…
- GSM9307965 RNA-seq ADCV, Adult ctrl, rep4 RNA-seq ADCV, Adult ctr…
- GSM9307966 RNA-seq ADCV, Adult nd1 cKO, rep1 RNA-seq ADCV, Adult nd1…
- GSM9307967 RNA-seq ADCV, Adult nd1 cKO, rep2 RNA-seq ADCV, Adult nd1…
- GSM9307968 RNA-seq ADCV, Adult nd1 cKO, rep3 RNA-seq ADCV, Adult nd1…
- GSM9307969 RNA-seq ADCV, Adult nd1 cKO, rep4 RNA-seq ADCV, Adult nd1…
- GSM9307970 RNA-seq ADCV, Adult nd2 cKO, rep1 RNA-seq ADCV, Adult nd2…
- GSM9307971 RNA-seq ADCV, Adult nd2 cKO, rep2 RNA-seq ADCV, Adult nd2…
- GSM9307972 RNA-seq ADCV, Adult nd2 cKO, rep3 RNA-seq ADCV, Adult nd2…
- GSM9307973 RNA-seq ADCV, Adult nd2 cKO, rep4 RNA-seq ADCV, Adult nd2…
- GSM9307974 RNA-seq ADCV, Adult nd1/2 dcKO, rep1 RNA-seq ADCV, Adult nd1…
- GSM9307975 RNA-seq ADCV, Adult nd1/2 dcKO, rep2 RNA-seq ADCV, Adult nd1…
- GSM9307976 RNA-seq ADCV, Adult nd1/2 dcKO, rep3 RNA-seq ADCV, Adult nd1…
- GSM9307977 RNA-seq ADCV, Adult nd1/2 dcKO, rep4 RNA-seq ADCV, Adult nd1…
- GSM9307978 RNA-seq ADCV, chromatin fraction, Adult homecage, rep1 RNA-seq ADCV, chromatin…
- GSM9307979 RNA-seq ADCV, chromatin fraction, Adult homecage, rep2 RNA-seq ADCV, chromatin…
- GSM9307980 RNA-seq ADCV, chromatin fraction, Adult homecage, rep3 RNA-seq ADCV, chromatin…
- GSM9307981 RNA-seq ADCV, chromatin fraction, Adult homecage, rep4 RNA-seq ADCV, chromatin…
- GSM9307982 RNA-seq ADCV, chromatin fraction, Adult 10m opto to 10m, rep1 RNA-seq ADCV, chromatin…
- GSM9307983 RNA-seq ADCV, chromatin fraction, Adult 10m opto to 10m, rep2 RNA-seq ADCV, chromatin…
- GSM9307984 RNA-seq ADCV, chromatin fraction, Adult 10m opto to 10m, rep3 RNA-seq ADCV, chromatin…
- GSM9307985 RNA-seq ADCV, chromatin fraction, Adult 10m opto to 10m, rep4 RNA-seq ADCV, chromatin…
- GSM9307986 RNA-seq ADCV, chromatin fraction, Adult homecage, rep5 RNA-seq ADCV, chromatin…
- GSM9307987 RNA-seq ADCV, chromatin fraction, Adult homecage, rep6 RNA-seq ADCV, chromatin…
- GSM9307988 RNA-seq ADCV, chromatin fraction, Adult homecage, rep7 RNA-seq ADCV, chromatin…
- GSM9307989 RNA-seq ADCV, chromatin fraction, Adult 30m opto to 40m, rep1 RNA-seq ADCV, chromatin…
- GSM9307990 RNA-seq ADCV, chromatin fraction, Adult 30m opto to 40m, rep2 RNA-seq ADCV, chromatin…
- GSM9307991 RNA-seq ADCV, chromatin fraction, Adult 30m opto to 1hr, rep1 RNA-seq ADCV, chromatin…
- GSM9307992 RNA-seq ADCV, chromatin fraction, Adult 30m opto to 1hr, rep2 RNA-seq ADCV, chromatin…
- GSM9307993 RNA-seq ADCV, chromatin fraction, Adult 30m opto to 1hr, rep3 RNA-seq ADCV, chromatin…
- GSM9307994 RNA-seq ADCV, chromatin fraction, Adult homecage, rep8 RNA-seq ADCV, chromatin…
- GSM9307995 RNA-seq ADCV, chromatin fraction, Adult homecage, rep9 RNA-seq ADCV, chromatin…
- GSM9307996 RNA-seq ADCV, chromatin fraction, Adult homecage, rep10 RNA-seq ADCV, chromatin…
- GSM9307997 RNA-seq ADCV, chromatin fraction, Adult homecage, rep11 RNA-seq ADCV, chromatin…
- GSM9307998 RNA-seq ADCV, chromatin fraction, Adult homecage, rep12 RNA-seq ADCV, chromatin…
- GSM9307999 RNA-seq ADCV, chromatin fraction, Adult homecage, rep13 RNA-seq ADCV, chromatin…
- GSM9308000 RNA-seq ADCV, chromatin fraction, Adult homecage, rep14 RNA-seq ADCV, chromatin…
- GSM9308001 RNA-seq ADCV, chromatin fraction, Adult 30m opto to 90m, rep1 RNA-seq ADCV, chromatin…
+ 33 more — browse all 73 samples with per-sample file links →
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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.