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Sex differences in microglial developmental gene expression programs

GSE99622 Mus musculus (mouse) RNA-seq (gene expression) 60 samples Submitted 2017/06/19 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 60 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
60 samples
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)
During normal neurodevelopment, microglia perform a range of different functions that are crucial for the proper development, circuit integration, and function of neurons. These functions include certain types of synaptic pruning during critical stages of neurodevelopment (Schafer et al., 2012), and the production of cytokines and chemokines during normal physiological tasks, proteins which are important for homeostasis in addition to immune defense (Avital et al., 2003; Goshen et al., 2007).
Read the full summary ↓
Microglia and the inflammatory cytokines they produce (e.g., in response to injury or infection) are also increasingly implicated in neural dysfunction during development and the risk of neuropsychiatric disorders. Increasing evidence suggests many neurological disorders emerge because of disrupted neuronal developmental trajectory (Marin, 2016). Considering the critical role of microglia for integration of neurons into their proper circuitry as well in proper synapse formation, there is a pressing need to understand the mechanisms underlying normal and abnormal microglia development, their interactions with specific neuronal subsets, and to understand the utility of these same analyses for human tissue. Moreover, as there are pronounced sex differences in the presentation of many neurological disorders, it is critical to understand these mechanisms in both males and females. Here we study developmental gene expression changes in male and female mice from E18 to P60. We isolated microglia from male and female hippocampi of mice from different developmental ages ranging from embryonic day 18 (E18) to postnatal day 60 (P60). Hippocampus was selected based on its importance to mental health, its marked vulnerability relative to other brain regions in response to diverse threats to homeostasis (epilepsy, stroke, and cardiac arrest (Fujioka et al., 2000; Petito, Feldmann, Pulsinelli, & Plum, 1987; Salmenpera, Kalviainen, Partanen, & Pitkanen, 1998; Sapolsky, Uno, Rebert, & Finch, 1990)), and due to evidence of morphological sex differences in microglial development in this region (Schwarz, Sholar, & Bilbo, 2012). It was found that developmental gene expression changes were more advanced in females at P60 and that treatment with LPS, a potent immune activator, could normalize developmental gene expression differences in males.
This dataset
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.

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 GSE99622_RAW.tar (it can run to tens of gigabytes).

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.

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 PRJNA388977 and SRA study SRP108497. Searching any of these in the dataset finder brings you back here.

Samples in this study

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