GEO series

Cartography of emergency myelopoiesis identifies dysregulated metabolism

GSE298048 Mus musculus (mouse) Single-cell RNA-seq 9 samples Submitted 2026/05/14 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 9 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: 9 samples: 8 distinct titles, 1 of them repeatedGroups 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.

Summary (written by the submitters)

Hematopoietic stem and progenitor cells (HSPC) respond to infections, inflammation, and regenerative challenges using cellular and molecular mechanisms termed emergency myelopoiesis (EM) pathways. However, it remains unclear whether all parts of the hematopoietic hierarchy are similarly activated by different EM inducers. Here, we generate a generalizable and comprehensive cell annotation method together with a refined quantitative model of hematopoietic differentiation using single cell RNA sequencing (scRNA-seq) of HSPCs, which we apply to a broad range of EM contexts.

Read the full summary ↓

We uncover multiple strategies to enhance myelopoiesis acting at different levels of the HSPC hierarchy, which are also associated with both unique and shared transcriptional response modules. In particular, we identify a myeloid progenitor-based signature associated with EM pathway engagement across multiple inflammatory challenges, which predicts outcome in both pediatric and adult human acute myeloid leukemia. Collectively, our work illuminates fundamental regulatory mechanisms in hematopoietic regeneration and identifies a common EM signature that informs outcome in disease contexts.

This dataset

Open GSE298048 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 GSE298048_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 PRJNA1267167 and SRA study SRP587326. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

8 distinct titles, 1 of them repeated

5FU_d8_LK ×2

How we read this: Read from 9 sample titles: 8 distinct titles with little repetition. 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

GSM9005914 Control_WBM
GSM9005915 5FU_d8_LK1
GSM9005916 5FU_d0_LSK.
GSM9005917 5FU_d0_LK.
GSM9005918 5FU_d8_LK2
GSM9005919 GCSF_d2_LK
GSM9005920 GCSF_d2_LSK
GSM9005921 GCSF_d4_LK
GSM9005922 GCSF_d4_LSK

Datasets on a similar topic

GSE296404 Cartography of emergency myelopoiesis identifies conserved molecular activation modules 15 samples shares myelopoiesis, cartography, identifies, emergency
GSE240912 Maternal IL-10 restricts fetal emergency myelopoiesis [Bulk RNA-seq] 36 samples shares myelopoiesis, emergency
GSE318312 Myc Driven Emergency Myelopoiesis Reprograms HPSC Metabolism 31 samples shares myelopoiesis, emergency
GSE291186 Emergency Myelopoiesis in Murine Arthritis Results in Cell-Intrinsic Changes in Dendritic Cell Development and Function 26 samples shares myelopoiesis, emergency
GSE240913 Maternal IL-10 restricts fetal emergency myelopoiesis [scRNA-seq] 10 samples shares myelopoiesis, emergency
GSE309251 Western diet-induced MASH in PWK/PhJ mice identifies disruptions in amino acid and sphingolipid metabolism contributing to cardiac dysfunction 347 samples shares identifies
GSE291440 GA-Camk2a mouse RNAseq data for the manuscript by Rezaei et al: Correction of dysregulated lipid metabolism normalizes gene expression in oligodendrocytes and prolongs lifespan in female poly-GA C9orf72 mouse model 21 samples shares dysregulated
GSE262778 Correction of dysregulated lipid metabolism normalizes gene expression in oligodendrocytes and prolongs lifespan in female poly-GA C9orf72 mouse model 15 samples shares dysregulated

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