GEO series

A Polyamine-mediated Posttranslational Modification Required for Macrophage Tissue Residency [Ribo-seq]

GSE290459 Mus musculus (mouse) RNA-seq (gene expression) 11 samples Submitted 2026/01/15 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 11 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: 11 samples: 3 × Input_DHPS_KO vs 3 × Input_DHPS_WT vs 3 × Ribo_DHPS_KO vs 2 × Ribo_DHPS_WTGroups 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: The transition from monocyte to tissue-resident macrophage requires DHPSNature · 2026

Summary (written by the submitters)

Tissue-resident macrophages (RTMs) form during embryogenesis, self-renew locally, and regulate tissue homeostasis by clearing dead cells and debris. During tissue damage, however, bone marrow-derived monocytes enter tissue sites and differentiate into RTM, repairing the tissue and replenishing macrophages in the niche. Universal cell-intrinsic mechanisms that control the monocyte to RTM transition remain elusive.

Read the full summary ↓

We investigated mice with myeloid cell deletions in deoxyhypusine synthase (DHPS), an enzyme that mediates the polyamine-dependent hypusine modification of the translation factor eIF5A, and found that DHPS is required for cell adhesion and signaling programs critical for RTMs. Without DHPS expression, immature tissue macrophages form, but RTM and associated homeostatic functions are lost. Thus, the polyamine-hypusine pathway is a global, tissue-agnostic program driving the differentiation trajectory of monocyte-derived macrophages into RTM.

Published in

The transition from monocyte to tissue-resident macrophage requires DHPS

Carrizo GE, Lin P, Lee SH et al. · Nature 2026 · PMID 41565804 · doi:10.1038/s41586-025-09972-2

This dataset

Open GSE290459 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 GSE290459_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 PRJNA1228073 and SRA study SRP566247. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41565804) ↗

Study design

3 × Input_DHPS_KO vs 3 × Input_DHPS_WT vs 3 × Ribo_DHPS_KO vs 2 × Ribo_DHPS_WT

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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

GSM8814872 Input_DHPS_KO_1 Input_DHPS_KO
GSM8814873 Input_DHPS_KO_2 Input_DHPS_KO
GSM8814874 Input_DHPS_KO_3 Input_DHPS_KO
GSM8814875 Input_DHPS_WT_1 Input_DHPS_WT
GSM8814876 Input_DHPS_WT_2 Input_DHPS_WT
GSM8814877 Input_DHPS_WT_3 Input_DHPS_WT
GSM8814878 Ribo_DHPS_KO_1 Ribo_DHPS_KO
GSM8814879 Ribo_DHPS_KO_2 Ribo_DHPS_KO
GSM8814880 Ribo_DHPS_KO_3 Ribo_DHPS_KO
GSM8814881 Ribo_DHPS_WT_2 Ribo_DHPS_WT
GSM8814882 Ribo_DHPS_WT_3 Ribo_DHPS_WT

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