← BioTransfer GEO Dataset Finder
GEO series

Transcriptional profiling of myeloid cells (CD11b) and astrocytes (ACSA2) from the striatum and the midbrain of control and parkinsonian animals in the MPTP mouse model

GSE244652 Mus musculus (mouse) RNA-seq (gene expression) 48 samples Submitted 2024/04/08 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 48 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
48 samples: 48 samples, each with a distinct title — no replicated groupsGroups 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
Nigrostriatal degeneration determines dynamics of glial inflammatory and phagocytic activityJournal of neuroinflammation · 2024
Summary (written by the submitters)
Neuroinflammation is a common hallmark of neurodegenerative diseases such as Parkinson’s disease (PD). Here, we questioned about the activation state of glial cells along the degeneration process of dopaminergic terminals in the striatum and loss of neuronal cell bodies in the midbrain. We hypothesized that MPTP administration pattern would produce different inflammatory responses that could modify the course of nigrostriatal degeneration.
Read the full summary ↓
To reproduce the dopaminergic impairment in a PD experimental mouse model, we used two different MPTP-administration patterns: subacute (sMPTP) and chronic (cMPTP). Bulk RNA sequencing of purified midbrain microglia/myeloid cells of sMPTP mice showed an anti-inflammatory phenotype, while midbrain microglia/myeloid cells of cMPTP mice showed a pro-inflammatory and phagocytic phenotype. Midbrain astrocytes presented a phagocytic phenotype in sMPTP mice. In the striatum, microglia presented a continuous pro-inflammatory state in sMPTP and cMPTP conditions. In this region, astrocytes presented a remarkable activated and phagocytic state in sMPTP mice which was attenuated with the chronicity of MPTP administration.
Published in
Nigrostriatal degeneration determines dynamics of glial inflammatory and phagocytic activity
Ayerra L, Abellanas MA, Basurco L et al. · Journal of neuroinflammation 2024 · PMID 38610019 · doi:10.1186/s12974-024-03091-x
This dataset
Open GSE244652 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 GSE244652_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 PRJNA1023966 and SRA study SRP464528. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38610019) ↗
Study design
48 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 48 sample titles: 48 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

+ 8 more — browse all 48 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.