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Sex-dependent niche responses modulate steady-state and regenerative hematopoiesis

GSE253024 Mus musculus (mouse) RNA-seq (gene expression) 10 samples Submitted 2025/01/01 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 10 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
10 samples: 5 × Bone Marrow cells, Male, vs 5 × Bone Marrow cells, Female,Groups 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
Sex-dependent niche responses modulate steady-state and regenerative hematopoiesisExperimental hematology · 2024
Summary (written by the submitters)
Hematopoietic stem cells (HSCs) adapt to organismal blood production needs. While it has been established that sexual dimorphism drives differential hematopoietic function in males vs. females, the mediators responsible for these effects remain unclear. Here, we characterize hematopoiesis in male and female mice at steady state and during regeneration following hematopoietic stem cell transplantation (HST).
Read the full summary ↓
We found that steady-state males possessed greater bone marrow (BM) hematopoietic stem and progenitor cell (HSPC) populations and varied in frequency for stromal populations. PCR analysis from stromal CD45(-)-purified BM cells demonstrated alterations in niche genes, including Ptn, IL6, Angpt1, Vcam1, and Spp1, together suggesting the male microenvironment is primed for HSC differentiation and mobilization. RNA sequencing of BM lineage(-) cells revealed differential expression of genes, like Hif1a and Aldh1, and corresponding cellular pathways—including those involving reactive oxygen species, oxidative phosphorylation, and Tnf-a signaling via NF-κB—underscoring male lineage(-) cells as more inflammatory and proliferative. To determine the functional outcomes of steady-state transcriptional differences we performed sex-matched and mismatched transplantation studies of lineage(-) donor cells into male and female recipients. We demonstrated a role for TNF-a-driven proliferation of male donor cells and Cxcl12-mediated homing into male recipients during short-term 56-day HST recovery. Serial transplantation of lineage(-) cells suggested the male short-term proliferative advantage may precede long-term disadvantages of inflammation-induced exhaustion. We show that sex-specific cellular and molecular signaling, marked by differing expression of niche factors and inflammatory mediators, shapes normal and regenerative hematopoiesis, with implications for the fundamental and clinical understanding of hematopoietic function.
Published in
Sex-dependent niche responses modulate steady-state and regenerative hematopoiesis
Chaudhary R, Smith JNP, Tiwari R et al. · Experimental hematology 2024 · PMID 38848877 · doi:10.1016/j.exphem.2024.104247
This dataset
Open GSE253024 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 GSE253024_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 PRJNA1063675 and SRA study SRP483364. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38848877) ↗
Study design
5 × Bone Marrow cells, Male, vs 5 × Bone Marrow cells, Female,

Supports a between-group comparison across 10 samples.

How we read this: 2 replicated groups read from 10 sample titles; they account for 10 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
Datasets on a similar topic

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