Mouse Microglia Cells

Microglia cells are a type of myeloid cells, related to macrophages, that are involved in the innate and adaptive defense of the central nervous system. Amongst others, they play a key role in the control of infections or the removal of necrotic neurons. An increased activation of microglia activity has also been found in several neurodegenerative disorders.


Here, we analyze a single cell data set of mouse microglia cells from different brain tissues (cerebellum, cortex, hippocampus and striatum). This dataset is part of a comprehensive single cell transcriptome atlas that was designed to study hallmarks of aging in a large variety of mouse tissues and organs (Tabula Muris Senis Project). It contains 8330 gene expression profiles of cells from mice with distinct age groups: 3 month, 18 month and 24 month. Here, we study molecular processes that are characteristic for the individual age groups.

Data set

The input for the single cell workflow is a gene expression matrix and a corresponding metadata file.

The raw gene counts of all microglia cells can be found here.
Corresponding metadata can be downloaded here.

Technical Background

For our analysis to work properly, we require a within-sample normalization, as we compare the expression values of different genes. This means that depending on the used scRNA-Seq protocol (e.g. for full-length sequencing protocols like SMART-seq2) a gene length normalization is required.

Supported methods

Currently, we offer two methods for gene-length normalization: TPM and GeTMM, and two methods for between-sample normalization: CPM and TMM. Based on the selected protocol, we already preselect suitable default parameters.



  • scRNA-Seq Protocol type: Based on full-length sequencing
  • Normalization method: log(TPM + 1) (includes length normalization)


  • Analyze the X most expressed genes per cell: 500

Over-representation analysis (ORA)

  • P-value strategy: Upper tailed
  • P-value adjustment method: Benjamini-Hochberg
  • Significance level: 0.05


  • Number of variable genes: 2000

Step-by-step slideshow

The following slideshow depicts the different analysis steps of the GeneTrail3 workflow.


In the following a few results of our conducted analysis are shown. In particular, we look at biological processes that distinguish cells from old mice (24 month) from cells of younger ones (18 month and 3 month).

Enriched biological processes

We see an enrichment of diverse biosynthesis processes (peptide, ATP, ..,), translation, and RNA processing.

Biosysthesis of peptides and ATP




RNA processing


Depleted processes

Additionally, we observe an depletion of autophagy, protein folding, and response to heat.



Protein folding


Response to heat