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A Novel Microglia-Specific Transcriptional Signatures Correlates with Behavioural Deficits in Neuropsychiatric Lupus (NP-SLE)

GSE288261 Mus musculus (mouse) RNA-seq (gene expression) 28 samples Submitted 2025/02/02 Platform GPL19057
At a glance

RNA-seq (gene expression) · mouse · 28 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
28 samples: 8 conditions, mostly with about 4 replicates eachGroups 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
A Novel Microglia-Specific Transcriptional Signature Correlates With Behavioral Deficits in Neuropsychiatric LupusFrontiers in immunology · 2020
Summary (written by the submitters)
Systemic lupus erythematosus (SLE) can present with neuropsychiatric manifestations, collectively termed NP-SLE. This study identifies a microglia-specific transcriptional signature in mouse models of NP-SLE. Through RNA-seq analysis of microglia and brain-infiltrating macrophages, we uncover an 18-gene 'NP-SLE signature' and its correlation with behavioral deficits.
Read the full summary ↓
We also observe enrichment of genes associated with disease-associated microglia (DAM), which have been implicated in neurodegenerative diseases. These findings suggest a critical role for microglia-intrinsic mechanisms in the onset of NP-SLE and provide new insights into the cellular and molecular pathways driving this disease.
Published in
A Novel Microglia-Specific Transcriptional Signature Correlates With Behavioral Deficits in Neuropsychiatric Lupus
Makinde HM, Winter DR, Procissi D et al. · Frontiers in immunology 2020 · PMID 32174913 · doi:10.3389/fimmu.2020.00230
This dataset
Open GSE288261 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 GSE288261_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 PRJNA1216644 and SRA study SRP560457. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 32174913) ↗
Study design
8 conditions, mostly with about 4 replicates each
Mus musculus Microglia Casp8flox/flox Female … ×4 Mus musculus Microglia CD11cCre Casp8flox/flo… ×4 Mus musculus Microglia Casp8flox/flox Female … ×4 Mus musculus Microglia CD11cCre Casp8flox/flo… ×4 Mus musculus Macrophage Casp8flox/flox Femal… ×3 Mus musculus Macrophage Casp8flox/flox Female… ×3 Mus musculus Macrophage CD11cCre Casp8flox/fl… ×3 Mus musculus Macrophage CD11cCre Casp8flox/fl… ×3

Supports a between-group comparison across 28 samples.

How we read this: 8 replicated groups read from 28 sample titles; they account for 28 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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