GEO series

Transcriptional profiling of murine oligodendrocyte precursor cells across the lifespan

GSE249268 Mus musculus (mouse) Single-cell RNA-seq 20 samples Submitted 2024/06/01 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 20 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. 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: 20 samples: 6 conditions, mostly in duplicateGroups 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)

Oligodendrocyte progenitor cells (OPCs) are highly dynamic, abundant glial cells of the central nervous system (CNS) that are responsible for generating myelinating oligodendrocytes during development. OPCs are also mobilized to form new myelin sheaths in the adult CNS in response to environmental and behavioral changes, and play a crucial role in regenerating myelin following demyelination (remyelination).

Read the full summary ↓

However, the rates of OPC proliferation and differentiation decline dramatically with aging, impairing homeostasis, remyelination, and potentially adaptive myelination during learning. To determine how aging influences OPCs, we generated a novel transgenic mouse line that expresses EGFP under the endogenous promoter/enhancer of Matrilin-4 (Matn4-mEGFP), allowing OPCs to be purified apart from perivascular and mural cells. OPCs isolated from the cerebral cortex of Matn4-mEGFP mice were subjected to single-cell RNA sequencing, providing enhanced resolution of transcriptional changes during key transitions from quiescence to proliferation and differentiation. Comparative analysis of OPCs isolated from mice aged 30 to 720 days, revealed that aging induces distinct inflammatory transcriptomic changes in OPCs in different states, including enhanced activation of HIF-1α and Wnt pathways. Inhibition of these pathways in acutely isolated OPCs from aged mice promoted their differentiation, suggesting that this enhanced signaling may contribute to the decreased regenerative potential of OPCs with aging. This Matn4-mEGFP mouse line and single-cell mRNA datasets of cortical OPCs across ages serve as a valuable reference to help define the molecular changes guiding their behavior in various physiological and pathological contexts.

This dataset

Open GSE249268 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 GSE249268_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 PRJNA1048408 and SRA study SRP475673. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

6 conditions, mostly in duplicate

OPC, P30, Male, ×4 OPC, P180, Female, ×3 OPC, P360, Male, ×3 OPC, P30, Female, ×2 OPC, P360, Female, ×2 OPC, P720, Female, ×2 OPC, P180, Male, ×1 OPC, P720, Female, 3 ×1 +2 more

Supports a between-group comparison across 16 samples.

How we read this: 6 replicated groups read from 20 sample titles; they account for 16 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

GSM7932612 OPC, P30, Female, 13 OPC, P30, Female,
GSM7932613 OPC, P30, Female, 2 OPC, P30, Female,
GSM7932614 OPC, P30, Male, 1 OPC, P30, Male,
GSM7932615 OPC, P30, Male, 10 OPC, P30, Male,
GSM7932616 OPC, P30, Male, 17 OPC, P30, Male,
GSM7932617 OPC, P30, Male, 4 OPC, P30, Male,
GSM7932618 OPC, P180, Female, 2 OPC, P180, Female,
GSM7932619 OPC, P180, Female, 3 OPC, P180, Female,
GSM7932620 OPC, P180, Female, 4 OPC, P180, Female,
GSM7932621 OPC, P180, Male, 1
GSM7932622 OPC, P360, Female, 2 OPC, P360, Female,
GSM7932623 OPC, P360, Female, 5 OPC, P360, Female,
GSM7932624 OPC, P360, Male, 1 OPC, P360, Male,
GSM7932625 OPC, P360, Male, 13 OPC, P360, Male,
GSM7932626 OPC, P360, Male, 8 OPC, P360, Male,
GSM7932627 OPC, P720, Female, 2 OPC, P720, Female,
GSM7932628 OPC, P720, Female, 3_16
GSM7932629 OPC, P720, Female, 9 OPC, P720, Female,
GSM7932630 OPC, P720, Male, 10
GSM7932631 OPC, P720, Male, 6_8

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