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Astrocytic Regulation of aberrant perineuronal net formation in Mecp2-null Neocortex

GSE306651 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/06/30 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 4 × E15.5 cortex, 12DIV, KO ACM, vs 4 × E15.5 cortex, 12DIV, NCM, vs 4 × E15.5 cortex, 12DIV, WT ACM,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
Astrocytic Regulation of Aberrant Perineuronal Net Formation in Mecp2-Null NeocortexJournal of neurochemistry · 2026
Summary (written by the submitters)
Rett syndrome (RTT), caused by mutations in MECP2, is a complex neurological disorder characterized by myriad physiological disruptions, including early closure of the critical period of developmental plasticity and precocious formation of perineuronal nets (PNNs). PNNs are lattice-like substructures of extracellular matrix (ECM) that enwrap specific subpopulations of neurons.
Read the full summary ↓
PNNs are essential in the modulation of neuronal plasticity and brain maturation, and their enzymatic disruption can partially restore plasticity in adults and improve memory. Although precocious PNN formation is well-established in RTT, there is little known of the cellular, molecular, or biochemical underpinnings of their precocious formation. Further, whether precocious PNN formation is due to cell-autonomous or non-cell-autonomous mechanisms is not fully understood. While PNNs form on subsets of neurons throughout the brain, astrocytes secrete many ECM components that form PNNs, and they play a central role in controlling closure of the critical period. We have found increased expression of both neuron- and astrocyte-derived PNN components in the developing Mecp2-null cortex, and demonstrate that PNNs are structurally and biochemically mature at an earlier developmental stage. Further, Mecp2-null astrocyte conditioned media induces the expression of the key PNN component Hapln1 and causes enhanced PNN formation on wildtype neurons. This suggests that Mecp2-null astrocytes play a key role in the precocious formation of PNNs in RTT. These results provide essential insight into the mechanisms and structure of aberrant PNNs in Mecp2-null cortex, and identify potential new avenues for targeted rescue or reversal of the precocious closing of the critical period in RTT.
Published in
Astrocytic Regulation of Aberrant Perineuronal Net Formation in Mecp2-Null Neocortex
Sinha A, Kowalchuk AM, Khatibi N et al. · Journal of neurochemistry 2026 · PMID 42375118 · doi:10.1111/jnc.70503
This dataset
Open GSE306651 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 GSE306651_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 PRJNA1311580 and SRA study SRP613702. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42375118) ↗
Study design
4 × E15.5 cortex, 12DIV, KO ACM, vs 4 × E15.5 cortex, 12DIV, NCM, vs 4 × E15.5 cortex, 12DIV, WT ACM,

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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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