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Effects of depletion of Irf8 and Mafb on gene expression of adult microglia and CNS border associtated macrophages (CAMs)

GSE269745 Mus musculus (mouse) RNA-seq (gene expression) 44 samples Submitted 2024/07/09 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 44 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
44 samples: 10 conditions, mostly with about 5 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
IRF8 and MAFB drive distinct transcriptional machineries in different resident macrophages of the central nervous systemCommunications biology · 2024
Summary (written by the submitters)
The central nervous system (CNS) includes anatomically distinct macrophage populations including parenchyma microglia and CNS-associated macrophages (CAMs). The stepwise development and specification of macrophage populations in the CNS rely on several key transcription factors, such as IRF8 and MAFB. In order to better understand the roles of IRF8 and MAFB for phenotypic determination of homeostatic microglia and CAMs, we performed quantitative bulk RNA sequencing of microglia and CAMs isolated from mouse models with myeloid cell-specific deletion of IRF8 or MAFB transcription factors.
Read the full summary ↓
We found the distinct transcriptional machinery, mediated by IRF8 and MAFB, which underlies the diversity of macrophages in the CNS.
Published in
IRF8 and MAFB drive distinct transcriptional machineries in different resident macrophages of the central nervous system
Yamasaki A, Imanishi I, Tanaka K et al. · Communications biology 2024 · PMID 39043941 · doi:10.1038/s42003-024-06607-6
This dataset
Open GSE269745 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 GSE269745_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 PRJNA1123600 and SRA study SRP513696. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39043941) ↗
Study design
10 conditions, mostly with about 5 replicates each
Irf8 control MG ×5 Irf8 ko MG ×5 Irf8 control CAMs ×5 Irf8 ko CAMs ×5 Mafb control MG ×5 Mafb control CAMs ×5 Mafb ko MG ×4 Mafb ko CAMs ×4 +2 more

Supports a between-group comparison across 44 samples.

How we read this: 10 replicated groups read from 44 sample titles; they account for 44 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

+ 4 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.