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An inducible genetic tool for tracking and manipulating specific microglial states in development and disease

GSE264553 Mus musculus (mouse) Single-cell RNA-seq 2634 samples Submitted 2024/06/11 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 2634 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: 2634 samples: 35 conditions, mostly with about 12 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: An inducible genetic tool to track and manipulate specific microglial states reveals their plasticity and roles in remyelinationImmunity · 2024

Summary (written by the submitters)

Recent single-cell RNA sequencing studies have revealed distinct microglial states in development and disease. These include proliferative region-associated microglia (PAM) in developing white matter and disease-associated microglia (DAM) prevalent in various neurodegenerative conditions. PAM and DAM share a similar core gene signature and other functional properties.

Read the full summary ↓

However, the extent of the dynamism and plasticity of these microglial states, as well as their functional significance, remains elusive, partly due to the lack of specific tools. Here, we report the generation of an inducible Cre driver line, Clec7a-CreERT2, designed to target PAM and DAM in the brain parenchyma. Utilizing this tool, we isolate and profile labeled cells during development and in several disease models, uncovering convergence and context-dependent differences in PAM/DAM gene expression. Through long-term tracking, we demonstrate surprising levels of plasticity in these microglial states. Lastly, we specifically deplete DAM in cuprizone-induced demyelination, revealing their roles in disease progression and recovery.

Published in

An inducible genetic tool to track and manipulate specific microglial states reveals their plasticity and roles in remyelination

Barclay KM, Abduljawad N, Cheng Z et al. · Immunity 2024 · PMID 38821054 · doi:10.1016/j.immuni.2024.05.005

This dataset

Open GSE264553 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 GSE264553_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 PRJNA1103143 and SRA study SRP503316. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38821054) ↗

Study design

35 conditions, mostly with about 12 replicates each

EAE,rep1,Neg,Plate1,A ×12 EAE,rep1,Neg,Plate1,B ×12 EAE,rep1,Neg,Plate1,C ×12 EAE,rep1,Neg,Plate1,D ×12 EAE,rep1,Neg,Plate1,F ×12 EAE,rep1,Neg,Plate1,G ×12 EAE,rep1,Neg,Plate2,A ×12 EAE,rep1,Neg,Plate2,B ×12 +27 more

Supports a between-group comparison across 400 samples.

How we read this: 35 replicated groups read from the first 400 of 2634 sample titles; they account for 400 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

GSM8219922 EAE,rep1,Neg,Plate1,A1 EAE,rep1,Neg,Plate1,A
GSM8219923 EAE,rep1,Neg,Plate1,A10 EAE,rep1,Neg,Plate1,A
GSM8219924 EAE,rep1,Neg,Plate1,A11 EAE,rep1,Neg,Plate1,A
GSM8219925 EAE,rep1,Neg,Plate1,A12 EAE,rep1,Neg,Plate1,A
GSM8219926 EAE,rep1,Neg,Plate1,A2 EAE,rep1,Neg,Plate1,A
GSM8219927 EAE,rep1,Neg,Plate1,A3 EAE,rep1,Neg,Plate1,A
GSM8219928 EAE,rep1,Neg,Plate1,A4 EAE,rep1,Neg,Plate1,A
GSM8219929 EAE,rep1,Neg,Plate1,A5 EAE,rep1,Neg,Plate1,A
GSM8219930 EAE,rep1,Neg,Plate1,A6 EAE,rep1,Neg,Plate1,A
GSM8219931 EAE,rep1,Neg,Plate1,A7 EAE,rep1,Neg,Plate1,A
GSM8219932 EAE,rep1,Neg,Plate1,A8 EAE,rep1,Neg,Plate1,A
GSM8219933 EAE,rep1,Neg,Plate1,A9 EAE,rep1,Neg,Plate1,A
GSM8219934 EAE,rep1,Neg,Plate1,B1 EAE,rep1,Neg,Plate1,B
GSM8219935 EAE,rep1,Neg,Plate1,B10 EAE,rep1,Neg,Plate1,B
GSM8219936 EAE,rep1,Neg,Plate1,B11 EAE,rep1,Neg,Plate1,B
GSM8219937 EAE,rep1,Neg,Plate1,B12 EAE,rep1,Neg,Plate1,B
GSM8219938 EAE,rep1,Neg,Plate1,B2 EAE,rep1,Neg,Plate1,B
GSM8219939 EAE,rep1,Neg,Plate1,B3 EAE,rep1,Neg,Plate1,B
GSM8219940 EAE,rep1,Neg,Plate1,B4 EAE,rep1,Neg,Plate1,B
GSM8219941 EAE,rep1,Neg,Plate1,B5 EAE,rep1,Neg,Plate1,B
GSM8219942 EAE,rep1,Neg,Plate1,B6 EAE,rep1,Neg,Plate1,B
GSM8219943 EAE,rep1,Neg,Plate1,B7 EAE,rep1,Neg,Plate1,B
GSM8219944 EAE,rep1,Neg,Plate1,B8 EAE,rep1,Neg,Plate1,B
GSM8219945 EAE,rep1,Neg,Plate1,B9 EAE,rep1,Neg,Plate1,B
GSM8219946 EAE,rep1,Neg,Plate1,C1 EAE,rep1,Neg,Plate1,C
GSM8219947 EAE,rep1,Neg,Plate1,C10 EAE,rep1,Neg,Plate1,C
GSM8219948 EAE,rep1,Neg,Plate1,C11 EAE,rep1,Neg,Plate1,C
GSM8219949 EAE,rep1,Neg,Plate1,C12 EAE,rep1,Neg,Plate1,C
GSM8219950 EAE,rep1,Neg,Plate1,C2 EAE,rep1,Neg,Plate1,C
GSM8219951 EAE,rep1,Neg,Plate1,C3 EAE,rep1,Neg,Plate1,C
GSM8219952 EAE,rep1,Neg,Plate1,C4 EAE,rep1,Neg,Plate1,C
GSM8219953 EAE,rep1,Neg,Plate1,C5 EAE,rep1,Neg,Plate1,C
GSM8219954 EAE,rep1,Neg,Plate1,C6 EAE,rep1,Neg,Plate1,C
GSM8219955 EAE,rep1,Neg,Plate1,C7 EAE,rep1,Neg,Plate1,C
GSM8219956 EAE,rep1,Neg,Plate1,C8 EAE,rep1,Neg,Plate1,C
GSM8219957 EAE,rep1,Neg,Plate1,C9 EAE,rep1,Neg,Plate1,C
GSM8219958 EAE,rep1,Neg,Plate1,D1 EAE,rep1,Neg,Plate1,D
GSM8219959 EAE,rep1,Neg,Plate1,D10 EAE,rep1,Neg,Plate1,D
GSM8219960 EAE,rep1,Neg,Plate1,D11 EAE,rep1,Neg,Plate1,D
GSM8219961 EAE,rep1,Neg,Plate1,D12 EAE,rep1,Neg,Plate1,D

+ 2594 more — browse all 2634 samples with per-sample file links →

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