GEO series

Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes

GSE272706 Mus musculus (mouse) RNA-seq (gene expression) 13 samples Submitted 2024/08/15 Platform GPL34328Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 13 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: 13 samples: 11 distinct titles, 2 of them repeatedGroups 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: Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypesbioRxiv : the preprint server for biology · 2025

Summary (written by the submitters)

The mammalian cerebral cortex comprises a complex neuronal network that maintains a delicate balance between excitatory neurons and inhibitory interneurons. Previous studies, including our own research, have shown that specific interneuron subtypes are closely associated with particular pyramidal neuron types, forming stereotyped local inhibitory microcircuits.

Read the full summary ↓

However, the developmental processes that establish these precise networks are not well understood. Here we show that pyramidal neuron types are instrumental in maintaining the terminal differentiation and survival of specific associated interneuron subtypes. In a wild-type cortex, the relative abundance of different interneuron subtypes aligns precisely with the pyramidal neuron types with which they synaptically target. In Fezf2 mutant cortex, characterized by the absence of layer 5 pyramidal tract neurons and an expansion of layer 6 intratelencephalic neurons, we observed a corresponding decrease in associated layer 5b interneurons and an increase in layer 6 subtypes. Interestingly, these shifts in composition are achieved through mechanisms that are specific to different interneuron types. While SST interneurons adjust their abundance to the change in pyramidal neuron prevalence through the regulation of programmed cell death, parvalbumin cells alter their identity. These findings illustrate two key strategies by which the dynamic interplay between pyramidal neurons and interneurons allows local microcircuits to be sculpted precisely. These insights underscored the precise roles of extrinsic signals from pyramidal cells in the establishment of interneuron diversity and their subsequent integration into local cortical microcircuits.

Published in

Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes

Wu SJ, Dai M, Yang SP et al. · bioRxiv : the preprint server for biology 2025 · PMID 39071350 · doi:10.1101/2024.07.20.604399

This dataset

Open GSE272706 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 GSE272706_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 PRJNA1138229 and SRA study SRP521710. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39071350) ↗

Study design

11 distinct titles, 2 of them repeated

P14 MGE Bax cKO ×2 P14 MGE Fezf2 KO Bax cKO ×2

How we read this: Read from 13 sample titles: 11 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

GSM8409498 P20 cortex interneuron
GSM8409499 P20 cortex interneuron Fezf2 KO
GSM8409500 P7 cortex interneuron Fezf2 KO
GSM8409501 P7 cortex interneuron Fezf2 HET
GSM8409502 P14 MGE Bax cHET
GSM8409503 P14 MGE Bax cKO rep1
GSM8409504 P14 MGE Bax cKO rep2
GSM8409505 P14 MGE Fezf2 KO Bax cKO rep1
GSM8409506 P14 MGE Fezf2 KO Bax cKO rep2
GSM8409507 P14 MGE Fezf2KO
GSM8409508 P2 MGE Fezf2 HET Bax cHET
GSM8409509 P2 MGE Fezf2 KO Bax cHET
GSM9291241 P20 cortical interneurons in control and in test condition with TeNT in Fezf2+ PNs

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