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Bone marrow niches orchestrate stem cell hierarchy and immune tolerance

GSE277668 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/10/31 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 12 samples, each with a distinct title — no replicated groupsGroups 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
Bone marrow niches orchestrate stem-cell hierarchy and immune toleranceNature · 2025
Summary (written by the submitters)
Stem cells reside in specialized microenvironments, termed niches, at several different locations within tissues1-3. The differential functions of heterogeneous stem cells and niches are important given increasing clinical applications of stem cell transplantation and immunotherapy. It remains unknown whether hierarchical structures amongst stem cells at distinct niches exist, and further control aspects of immune tolerance.
Read the full summary ↓
Here, we propose novel hierarchical arrangements within hematopoietic stem cells (HSCs) and bone marrow (BM) niches, that dictate both regenerative potential and immune privilege. High level nitric oxide-generating (NOHi) HSCs are refractory to immune attack and exhibit "delayed" albeit robust long-term reconstitution. Such highly immune privileged, primitive NOHi HSCs colocalize with distinctive capillaries, characterized by primary ciliated endothelium and high levels of the immune checkpoint molecule CD200. These capillaries regulate the regenerative functions of NOHi HSCs through ciliary protein IFT20/CD200/eNOS/autophagy signals, further mediating immune protection. Notably, previously described niche constituents, sinusoidal cells and Type H vessels2-10, co-localize with less immune privileged and less potent NOLow HSCs. Therefore, we have identified highly immune privileged, "late-rising" primitive HSCs and characterized their immunoprotective niches constituted of specialized vascular domains. Our studies suggest the niche may orchestrate hierarchy in stem cells and immune tolerance, delineating future immunotherapeutic targets.
Published in
Bone marrow niches orchestrate stem-cell hierarchy and immune tolerance
Furuhashi K, Kakiuchi M, Ueda R et al. · Nature 2025 · PMID 39743593 · doi:10.1038/s41586-024-08352-6
This dataset
Open GSE277668 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 GSE277668_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 PRJNA1163324 and SRA study SRP533854. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39743593) ↗
Study design
12 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 12 sample titles: 12 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
Datasets on a similar topic

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