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BMP9 and BMP10 coordinate liver cellular crosstalk to maintain liver health

GSE244429 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/09/26 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 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
GDF2 and BMP10 coordinate liver cellular crosstalk to maintain liver healtheLife · 2024
Summary (written by the submitters)
The liver is a largest solid organ in the body and is majorly composed of HCs, ECs, KCs, and HSCs, which spatially interact and cooperate each other to maintain liver homeostasis. However, the complexity and molecular mechanisms underlying the crosstalk between these different cell types remain to be revealed. Here, we generated mice with conditional deletion of Bmp9/10 in different liver cell types and demonstrated that HSCs was the major source of BMP9 and BMP10 in the liver.
Read the full summary ↓
Using transgenic ALK1 (receptor for BMP9/10) reporter mice, we found that ALK1 is expressed on KCs and ECs other than HCs and HSCs. KCs from Bmp9/10HSC-KO (conditional deletion of Bmp9/10 from HSCs) mice lost their signature genes expression, such as ID1/3, CLEC4F, VSIG4 and CLEC2, and were replaced by monocyte-derived macrophages. ECs from Bmp9/10HSC-KO mice also lost their identity and were transdifferentiated to continuous ECs, ultimately leading to collagen IV deposition and liver fibrosis. Hepatic ECs expressed several angiocrine factors, such as BMP2, BMP6, Wnt2 and Rspo3, to regulate liver iron metabolism and metabolic zonation. We found that these angiocrine factors were significantly decreased in ECs from Bmp9/10HSC-KO mice, which further resulted in liver iron overload and disruption of HCs zonation. In addition, focal fatty liver spontaneously occurred in Bmp9/10HSC-KO mice at the age of 28W. In summary, we demonstrated that HSCs play a central role in mediating liver cell-cell crosstalk via production of BMP9/10 to maintain liver health.
Published in
GDF2 and BMP10 coordinate liver cellular crosstalk to maintain liver health
Zhao D, Huang Z, Li X et al. · eLife 2024 · PMID 39453386 · doi:10.7554/eLife.95811
This dataset
Open GSE244429 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 GSE244429_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 PRJNA1023032 and SRA study SRP464095. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39453386) ↗
Study design
8 conditions, mostly in triplicate
Liver macrophages from BMP9/10 control mice ×3 Liver macrophages from Bmp9/10-HSC-KO mice ×3 Liver macrophages from Smad4FF ×3 Liver macrophages from Smad4FF cKO ×3 ECs from control mice ×3 ECs from Bmp9/10-HSC-KO mice ×3 Liver tissue from control mice ×3 Liver tissue from Bmp9/10-HSC-KO mice ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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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