GEO series

Adult skull bone marrow is an expanding and resilient hematopoietic reservoir

GSE275179 Mus musculus (mouse) RNA-seq (gene expression) 19 samples Submitted 2024/08/22 Platform GPL19057

At a glance

RNA-seq (gene expression) · mouse · 19 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: 19 samples: 16 distinct titles, 2 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.
Paper: Adult skull bone marrow is an expanding and resilient haematopoietic reservoirNature · 2024

Summary (written by the submitters)

The bone marrow microenvironment is a critical regulator of hematopoietic stem cell self-renewal and fate. While it is appreciated that aging, chronic inflammation and other insults compromise bone marrow function and thereby negatively affect hematopoiesis, it is not known whether different bone compartments exhibit distinct microenvironmental properties and functional resilience.

Read the full summary ↓

Here, we have employed imaging, pharmacological approaches, and mouse genetics to uncover specialized and highly surprising properties of bone marrow in adult and aging skull. Specifically, we show that the skull bone marrow undergoes lifelong expansion involving vascular growth, which results in an increasing contribution to total hematopoietic output. Furthermore, skull is largely protected against major hallmarks of aging, including upregulation of pro-inflammatory cytokines, adipogenesis and loss of vascular integrity. Striking dynamic and rapid changes to the skull vasculature and bone marrow are induced by physiological alterations, namely pregnancy, but also pathological challenges, such as stroke and experimental chronic myeloid leukemia. These responses are highly distinct from femur, the most extensively studied bone marrow compartment. We propose that skull harbors a protected and dynamically expanding bone marrow microenvironment, which is relevant for experimental studies but, potentially, also clinical treatments in humans.

Published in

Adult skull bone marrow is an expanding and resilient haematopoietic reservoir

Koh BI, Mohanakrishnan V, Jeong HW et al. · Nature 2024 · PMID 39537918 · doi:10.1038/s41586-024-08163-9

This dataset

Open GSE275179 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 GSE275179_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 PRJNA1149727 and SRA study SRP527318. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39537918) ↗

Study design

16 distinct titles, 2 of them repeated

Old Skull All ×3 Old Femur All ×2

How we read this: Read from 19 sample titles: 16 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

GSM8472468 Old Femur All Replicate 1
GSM8472469 Old Skull All Replicate 1
GSM8472470 Old Femur Stromal
GSM8472471 Old Skull Stromal
GSM8472472 Old Femur HSPC
GSM8472473 Old Skull HSPC
GSM8472474 Young Femur HSPC
GSM8472475 Young Skull HSPC
GSM8472476 Young Femur Stromal
GSM8472477 Young Femur Stromal Haem
GSM8472478 Young Skull Stromal Haem
GSM8472479 Young Skull Frontal
GSM8472480 Young Skull Parietal
GSM8472481 Young Skull Interparietal
GSM8472482 Old Skull All Replicate 2
GSM8472483 Old Femur All Replicate 2
GSM8472484 Old Skull All Replicate 3
GSM8472485 Young Femur All
GSM8472486 Young Skull All

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