GEO series

Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction

GSE269499 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2024/06/14 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 28 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: 28 samples: 28 samples, each with a distinct title — no replicated groupsGroups 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: Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interactioniScience · 2024

Summary (written by the submitters)

Reliable representations of information regarding complex behaviors including social interactions require the coordinated activity of heterogeneous cell types within distributed brain regions. Activity in the medial prefrontal cortex is critical in regulating social behavior, but our understanding of the specific cell types which comprise the social ensemble has been limited by available mouse lines and molecular tagging strategies which rely on the expression of a single marker gene.

Read the full summary ↓

Here we sought to quantify the heterogeneous neuronal populations which are recruited during social interaction in parallel in a non-biased manner and determine how distinct cell types are differentially active during social interactions. We identify distinct populations of prefrontal neurons activated by social interaction by quantification of immediate early gene (IEG) expression in transcriptomically clustered neurons. This approach revealed variability in the recruitment of different excitatory and inhibitory populations within the medial prefrontal cortex. Furthermore, evaluation of the populations of IEGs recruited following social interaction revealed both cell-type and region-specific transcriptional programs, suggesting that reliance on a single molecular marker is insufficient to quantify activation across all cell types. Our findings provide a comprehensive description of cell-type specific transcriptional programs invoked by social interactions and reveal new insights into the heterogeneous neuronal populations which compose the social ensemble

Published in

Distinct transcriptional programs define a heterogeneous neuronal ensemble for social interaction

Walker H, Frost NA · iScience 2024 · PMID 39045099 · doi:10.1016/j.isci.2024.110355

This dataset

Open GSE269499 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 GSE269499_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 PRJNA1122152 and SRA study SRP512939. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39045099) ↗

Study design

28 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 28 sample titles: 28 distinct titles with little repetition. 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

GSM8316790 20251x1, WT PFC, Social 35, M
GSM8316791 20375x6, WT PFC, Not, F
GSM8316792 20521x1, WT PFC, Social 35, F
GSM8316793 20523x1, WT PFC, Not, M
GSM8316794 19957x3, WT PFC, Not, M
GSM8316795 20042x1, WT PFC, Social 35, M
GSM8316796 20042x2, WT PFC, Not, M
GSM8316797 20042x3, WT PFC, Social 35, F
GSM8316798 20042x4, WT PFC, Not, F
GSM8316799 20042x5, WT PFC, Social 35, F
GSM8316800 20042x6, WT PFC, Not, F
GSM8316801 20778X1, WT PFC, Social 10, M
GSM8316802 20778X3, WT PFC, Social 10, F
GSM8316803 20778X5, WT PFC, Social 10, F
GSM8316804 20251x3, WT Cerebellum, Social 35, M
GSM8316805 20375x10, WT Cerebellum, Not, F
GSM8316806 20521x4, WT Cerebellum, Social 35, F
GSM8316807 20523x4, WT Cerebellum, Not, M
GSM8316808 19957x2, WT Cerebellum, Social 35, M
GSM8316809 20053x1, WT Cerebellum, Social 35, M
GSM8316810 20053x2, WT Cerebellum, Not, M
GSM8316811 20053x3, WT Cerebellum, Social 35, F
GSM8316812 20053x4, WT Cerebellum, Not, F
GSM8316813 20053x5, WT Cerebellum, Social 35, F
GSM8316814 20053x6, WT Cerebellum, Not, F
GSM8316815 20778X2, WT Cerebellum, Social 10, M
GSM8316816 20778X4, WT Cerebellum, Social 10, F
GSM8316817 20778X6, WT Cerebellum, Social 10, F

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