GEO series

RNA sequencing data of dural macrophages isolated from brains of Cx3cr1-GFP mice at different ages.

GSE277981 Mus musculus (mouse) Single-cell RNA-seq 15 samples Submitted 2024/12/20 Platform GPL15103

At a glance

Single-cell RNA-seq · mouse · 15 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: 15 samples: 5 conditions, mostly in triplicateGroups 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: Extrasinusoidal macrophages are a distinct subset of immunologically active dural macrophagesScience immunology · 2024

Summary (written by the submitters)

While macrophages in the meningeal compartments of the central nervous system (CNS) has been comprehensively characterized under steady state, studying their contribution to physiological and pathological processes has been severely hampered by the lack of specific targeting tools in vivo. Recent findings have shown that the dural sinus and its adjacent lymphatic vessels act as a neuroimmune interface.

Read the full summary ↓

Notably, the cellular and functional heterogeneity of extrasinusoidal dural macrophages outside this immune hub is currently unclear. Therefore, we comprehensively characterized these cells using single-cell transcriptomics, fate mapping, confocal imaging, clonal analysis and transgenic mouse lines. Extrasinusoidal dural macrophages were clearly distinct from leptomeningeal and CNS parenchymal macrophages in terms of their origin, expansion kinetics and transcriptional profiles. Lastly, functional studies demonstrated that during autoimmune neuroinflammation, extrasinusoidal dural macrophages perform efferocytosis of granulocytes. Our results highlight a previously unappreciated myeloid cell diversity and provide insights into the brain’s innate immune system.

Published in

Extrasinusoidal macrophages are a distinct subset of immunologically active dural macrophages

Amann L, Fell A, Monaco G et al. · Science immunology 2024 · PMID 39705337 · doi:10.1126/sciimmunol.adh1129

This dataset

Open GSE277981 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 GSE277981_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 PRJNA1165151 and SRA study SRP534660. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39705337) ↗

Study design

5 conditions, mostly in triplicate

CD206pos_8W_14 ×3 CD206pos_3W_15 ×3 CD206pos_d10_16 ×3 CD206pos_d3_17 ×3 CD206pos_E14.5_18 ×3

Supports a between-group comparison across 15 samples.

How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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

GSM8536713 CD206pos_8W_14_4 CD206pos_8W_14
GSM8536714 CD206pos_8W_14_5 CD206pos_8W_14
GSM8536715 CD206pos_8W_14_6 CD206pos_8W_14
GSM8536716 CD206pos_3W_15_1 CD206pos_3W_15
GSM8536717 CD206pos_3W_15_2 CD206pos_3W_15
GSM8536718 CD206pos_3W_15_3 CD206pos_3W_15
GSM8536719 CD206pos_d10_16_1 CD206pos_d10_16
GSM8536720 CD206pos_d10_16_2 CD206pos_d10_16
GSM8536721 CD206pos_d10_16_3 CD206pos_d10_16
GSM8536722 CD206pos_d3_17_1 CD206pos_d3_17
GSM8536723 CD206pos_d3_17_2 CD206pos_d3_17
GSM8536724 CD206pos_d3_17_3 CD206pos_d3_17
GSM8536725 CD206pos_E14.5_18_1 CD206pos_E14.5_18
GSM8536726 CD206pos_E14.5_18_2 CD206pos_E14.5_18
GSM8536727 CD206pos_E14.5_18_3 CD206pos_E14.5_18

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