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Cell type-specific dysregulation of gene expression due to Chd8 loss of function during mouse cortical development [bulk RNA-seq]

GSE273270 Mus musculus (mouse) Single-nucleus RNA-seq 36 samples Submitted 2024/08/14 Platform GPL24247
At a glance

Single-nucleus RNA-seq · mouse · 36 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
36 samples: 12 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
Cell type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical developmentbioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Disruptive variants in the chromodomain helicase CHD8, which acts as a transcriptional regulator during neurodevelopment, are strongly associated with risk for autism spectrum disorder (ASD). Loss of CHD8 function is hypothesized to perturb gene regulatory networks in the developing brain, thereby contributing to ASD etiology. However, insight into the cell type-specific transcriptional effects of CHD8 loss of function remains limited.
Read the full summary ↓
We used single-cell and single-nucleus RNA-sequencing to globally profile gene expression and identify dysregulated genes in the embryonic and juvenile wild type and Chd8+/− mouse cortex, respectively. Chd8 and other ASD risk-associated genes showed a convergent expression trajectory that was largely conserved between the mouse and human developing cortex, increasing from the progenitor zones to the cortical plate. Genes associated with risk for neurodevelopmental disorders and genes involved in neuron projection development, chromatin remodeling, signaling, and migration were dysregulated in Chd8+/− embryonic day (E) 12.5 radial glia. Genes implicated in synaptic organization and activity were dysregulated in Chd8+/− postnatal day (P) 25 deep- and upper-layer excitatory neurons, suggesting a delay in synaptic maturation or impaired synaptogenesis due to CHD8 loss of function. Our findings reveal a complex pattern of transcriptional dysregulation in Chd8+/− developing cortex, potentially with distinct biological impacts on progenitors and maturing neurons in the excitatory neuronal lineage.
Published in
Cell type-specific dysregulation of gene expression due to Chd8 haploinsufficiency during mouse cortical development
Yim KM, Baumgartner M, Krenzer M et al. · bioRxiv : the preprint server for biology 2024 · PMID 39185167 · doi:10.1101/2024.08.14.608000
This dataset
Open GSE273270 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 GSE273270_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 PRJNA1141139 and SRA study SRP522679. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39185167) ↗
Study design
12 conditions, mostly in triplicate
E12.5 dorsal telencephalon, wild type male, b… ×3 E12.5 dorsal telencephalon, wild type female,… ×3 E12.5 dorsal telencephalon, Chd8 het male, bu… ×3 E12.5 dorsal telencephalon, Chd8 het female, … ×3 E17.5 dorsal telencephalon, wild type male, b… ×3 E17.5 dorsal telencephalon, wild type female,… ×3 E17.5 dorsal telencephalon, Chd8 het male, bu… ×3 E17.5 dorsal telencephalon, Chd8 het female, … ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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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