GEO series

Maternal IL-10 restricts fetal emergency myelopoiesis [Bulk RNA-seq]

GSE240912 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2024/02/29 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 36 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: 36 samples: 12 conditions, mostly in triplicateGroups 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: Maternal inflammation regulates fetal emergency myelopoiesisCell · 2024

Summary (written by the submitters)

We investigated how late fetal liver (FL) mouse hematopoieitic stem and progenitor cells (HSPC) respond to inflammation, with the hypothesis that deficits in engagement of emergency myelopoiesis (EM) pathways could limit neutrophil output and contribute to perinatal neutropenia, ultimately explaining the susceptibility of neonates to inflammation and infection.

Read the full summary ↓

We show that fetal HSPCs are biased toward erythroid and lymphoid cell production at steady state and fail to mount classical EM responses in vivo. Despite being capable of responding to EM-inducing stimuli in vitro, we find that maternal factors like interleukin-10 (IL-10) restrict fetal HSPCs from activating EM pathways in utero. Accordingly, we find that loss of maternal IL-10 restores EM activation in fetal HSPCs but at a cost of premature parturition. These results reveal the evolutionary trade-off inherent in maternal anti-inflammatory responses that maintain pregnancy but render the fetus susceptible to infection.

Published in

Maternal inflammation regulates fetal emergency myelopoiesis

Collins A, Swann JW, Proven MA et al. · Cell 2024 · PMID 38428422 · doi:10.1016/j.cell.2024.02.002

This dataset

Open GSE240912 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 GSE240912_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 PRJNA1005684 and SRA study SRP455254. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38428422) ↗

Study design

12 conditions, mostly in triplicate

2 wk HSC biol ×3 2 wk MPP2 biol ×3 2 wk MPP3 biol ×3 2 wk MPP4 biol ×3 Adult HSC biol ×3 Adult MPP2 biol ×3 Adult MPP3 biol ×3 Adult MPP4 biol ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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

GSM7711976 2 wk HSC biol rep 1 2 wk HSC biol
GSM7711977 2 wk HSC biol rep 2 2 wk HSC biol
GSM7711978 2 wk HSC biol rep 3 2 wk HSC biol
GSM7711979 2 wk MPP2 biol rep 1 2 wk MPP2 biol
GSM7711980 2 wk MPP2 biol rep 2 2 wk MPP2 biol
GSM7711981 2 wk MPP2 biol rep 3 2 wk MPP2 biol
GSM7711982 2 wk MPP3 biol rep 1 2 wk MPP3 biol
GSM7711983 2 wk MPP3 biol rep 2 2 wk MPP3 biol
GSM7711984 2 wk MPP3 biol rep 3 2 wk MPP3 biol
GSM7711985 2 wk MPP4 biol rep 1 2 wk MPP4 biol
GSM7711986 2 wk MPP4 biol rep 2 2 wk MPP4 biol
GSM7711987 2 wk MPP4 biol rep 3 2 wk MPP4 biol
GSM7711988 Adult HSC biol rep 1 Adult HSC biol
GSM7711989 Adult HSC biol rep 2 Adult HSC biol
GSM7711990 Adult HSC biol rep 3 Adult HSC biol
GSM7711991 Adult MPP2 biol rep 1 Adult MPP2 biol
GSM7711992 Adult MPP2 biol rep 2 Adult MPP2 biol
GSM7711993 Adult MPP2 biol rep 3 Adult MPP2 biol
GSM7711994 Adult MPP3 biol rep 1 Adult MPP3 biol
GSM7711995 Adult MPP3 biol rep 2 Adult MPP3 biol
GSM7711996 Adult MPP3 biol rep 3 Adult MPP3 biol
GSM7711997 Adult MPP4 biol rep 1 Adult MPP4 biol
GSM7711998 Adult MPP4 biol rep 2 Adult MPP4 biol
GSM7711999 Adult MPP4 biol rep 3 Adult MPP4 biol
GSM7712000 E18 HSC biol rep 1 E18 HSC biol
GSM7712001 E18 HSC biol rep 2 E18 HSC biol
GSM7712002 E18 HSC biol rep 3 E18 HSC biol
GSM7712003 E18 MPP2 biol rep 1 E18 MPP2 biol
GSM7712004 E18 MPP2 biol rep 2 E18 MPP2 biol
GSM7712005 E18 MPP2 biol rep 3 E18 MPP2 biol
GSM7712006 E18 MPP3 biol rep 1 E18 MPP3 biol
GSM7712007 E18 MPP3 biol rep 2 E18 MPP3 biol
GSM7712008 E18 MPP3 biol rep 3 E18 MPP3 biol
GSM7712009 E18 MPP4 biol rep 1 E18 MPP4 biol
GSM7712010 E18 MPP4 biol rep 2 E18 MPP4 biol
GSM7712011 E18 MPP4 biol rep 3 E18 MPP4 biol

Datasets on a similar topic

GSE240913 Maternal IL-10 restricts fetal emergency myelopoiesis [scRNA-seq] 10 samples shares il-10, myelopoiesis, restricts, emergency, maternal, rna-seq, fetal
GSE240915 Maternal IL-10 restricts fetal emergency myelopoiesis 50 samples shares il-10, myelopoiesis, restricts, emergency, maternal, fetal
GSE272933 Pregnancy Restricts an Age-Driven Accumulation of Hybrid Cells in the Mammary Gland [bulk RNA-Seq] 18 samples shares restricts, rna-seq, bulk
GSE283694 Bacterial immunotherapy leveraging IL-10R hysteresis for both phagocytosis evasion and tumor immunity revitalization [RNA-seq] 21 samples shares il-10, rna-seq
GSE306262 Astrocyte glucocorticoid receptor signaling restricts neuronal plasticity [RNA-seq] 40 samples shares restricts, rna-seq
GSE291186 Emergency Myelopoiesis in Murine Arthritis Results in Cell-Intrinsic Changes in Dendritic Cell Development and Function 26 samples shares myelopoiesis, emergency
GSE276826 An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation (G320D RNA-Seq) 18 samples shares myelopoiesis, rna-seq
GSE276829 An IL-33–LMO4 axis instructs type 2 myelopoiesis via GATA factor re-allocation (BMT LMO4 RNA-Seq) 18 samples shares myelopoiesis, rna-seq

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