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Female cortical cellular mosaicism underlies shared MeCP2 and PCB impacted gene pathways

GSE316011 Mus musculus (mouse) Single-nucleus RNA-seq 16 samples Submitted 2026/01/31 Platform GPL24247

At a glance

Single-nucleus RNA-seq · mouse · 16 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 16 samples: 2 × 27_PCB_HET vs 2 × 30_VEHICLE_WT vs 2 × 37_PCB_WT vs 2 × 40_VEHICLE_HETGroups 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.

Summary (written by the submitters)

Etiologies of neurodevelopmental disorders involve genes and environment however their interactions are understudied. Rett Syndrome (RTT) is an X-linked, dominant neurodevelopmental disorder caused by mutations in MECP2, encoding the epigenetic regulator methyl CpG binding protein. The variability in severity and timing of progression in RTT, influenced by factors including mutation type, genetic background, and X-chromosome inactivation patterns, suggests potential interaction with environmental neurotoxicants such as lipophilic polychlorinated biphenyls (PCBs).

Read the full summary ↓

Understanding these gene-by-environment interactions has broader implications for neurodevelopmental disorders, as MeCP2 dysregulation occurs in ~70% of autism spectrum disorder cases. To understand shared mechanisms, we exposed WT and Mecp2e1-/+ female mice to a human-relevant PCB mixture and dose, then performed single-nucleus 5’ RNA-seq from cortex. We identified significant overlap in dysregulated genes and 71 shared pathways between the effects of PCB exposure and MeCP2 mutation, and co-mitigation of their transcriptional impacts. PCBs influenced the non-cell-autonomous transcriptional effects of MeCP2 mutations in wild-type-expressing neurons within the mosaic mutant female cortex in both mouse and human, suggesting that the interactions predominantly involve homeostatic gene networks.

This dataset

Open GSE316011 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 GSE316011_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1400445 and SRA study SRP660959. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

2 × 27_PCB_HET vs 2 × 30_VEHICLE_WT vs 2 × 37_PCB_WT vs 2 × 40_VEHICLE_HET

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 8 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

GSM9443270 24_PCB_WT
GSM9443271 25_VEHICLE_WT
GSM9443272 27_PCB_HET_2 27_PCB_HET
GSM9443273 27_PCB_HET 27_PCB_HET
GSM9443274 28_VEHICLE_HET
GSM9443275 29_VEHICLE_WT
GSM9443276 30_VEHICLE_WT_2 30_VEHICLE_WT
GSM9443277 30_VEHICLE_WT 30_VEHICLE_WT
GSM9443278 31_PCB_WT
GSM9443279 36_PCB_HET
GSM9443280 37_PCB_WT_2 37_PCB_WT
GSM9443281 37_PCB_WT 37_PCB_WT
GSM9443282 38_VEHICLE_HET
GSM9443283 39_PCB_HET
GSM9443284 40_VEHICLE_HET_2 40_VEHICLE_HET
GSM9443285 40_VEHICLE_HET 40_VEHICLE_HET

Datasets on a similar topic

GSE315769 Sex and tissue resolved co-expression networks reveal a female placental–brain axis protective against prenatal PCB exposure 192 samples shares pcb, female
GSE295530 MeCP2 stabilizes the glucocorticoid system in active chromatin regions [RNA-seq] 723 samples shares mecp2
GSE246119 Dynamic dysregulation of the transcriptome upon deletion of Mecp2 in adult mice 144 samples shares mecp2
GSE300534 Brain Mecp2 Genetic Dosage and Gene Therapy Shape Multi-omics Signatures and Biomarkers in Rett Syndrome [1] 137 samples shares mecp2
GSE300536 Brain Mecp2 Genetic Dosage and Gene Therapy Shape Multi-omics Signatures and Biomarkers in Rett Syndrome [2] 137 samples shares mecp2
GSE237084 Non-CG DNA methylation and MeCP2 stabilize repeated tuning of long genes that distinguish closely related neuron types [RNA-seq] 38 samples shares mecp2
GSE299346 Mecp2 stabilizes the glucocorticoid system in active chromatin regions [scRNA-Seq] 36 samples shares mecp2
GSE244388 PCB126 Modifies the Murine Hepatic Transcriptome and Metallome to Promote Alcohol-associated Liver Disease Pathogenesis 24 samples shares pcb

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