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Nr4a1 regulates cell-specific transcriptional programs in inhibitory GABAergic interneurons

GSE263082 Mus musculus (mouse) RNA-seq (gene expression) 34 samples Submitted 2024/06/05 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 34 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
34 samples: 11 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
Nr4a1 regulates cell-specific transcriptional programs in inhibitory GABAergic interneuronsNeuron · 2024
Summary (written by the submitters)
The patterns of synaptic connectivity and physiological properties of diverse neuron types are shaped by distinct gene sets. Our study demonstrates that, in the mouse forebrain, the transcriptional profiles of inhibitory GABAergic interneurons are regulated by Nr4a1, an orphan nuclear receptor whose expression is transiently induced by sensory experiences and is required for normal learning.
Read the full summary ↓
Nr4a1 exerts contrasting effects on the local axonal wiring of Parvalbumin- and Somatostatin-positive interneurons, which innervate different subcellular domains of their postsynaptic partners. The loss of Nr4a1 activity in these interneurons results in bidirectional, cell-type-specific transcriptional switches across multiple gene families, including those involved in surface adhesion and repulsion. Our findings reveal that combinatorial synaptic organizing codes are surprisingly flexible and highlight a mechanism by which inducible transcription factors can influence neural circuit structure and function.
Published in
Nr4a1 regulates cell-specific transcriptional programs in inhibitory GABAergic interneurons
Huang M, Pieraut S, Cao J et al. · Neuron 2024 · PMID 38754414 · doi:10.1016/j.neuron.2024.03.018
This dataset
Open GSE263082 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 GSE263082_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 PRJNA1095557 and SRA study SRP499394. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38754414) ↗
Study design
11 conditions, mostly in triplicate
Batch1_PVR_PTZ ×4 Batch2_SST_Saline ×4 Batch1_PVR_Saline ×3 Batch2_SST_PTZ ×3 Batch3_PVR_CFC ×3 Batch3_PVR_HC ×3 Batch3_PVNR ×3 Batch4_SST_HC ×3 +3 more

Supports a between-group comparison across 34 samples.

How we read this: 11 replicated groups read from 34 sample titles; they account for 34 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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