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SREBP2 restricts osteoclast differentiation and activity by regulating IRF7 and limits inflammatory bone erosion.

GSE172007 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/09/30 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 16 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
16 samples: 8 conditions, mostly in duplicateGroups 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
SREBP2 restricts osteoclast differentiation and activity by regulating IRF7 and limits inflammatory bone erosionBone research · 2024
Summary (written by the submitters)
Osteoclasts are multinucleated bone resorbing cells, and their dysregulation leads to pathological bone destruction. Osteoclast formation must be tightly regulated to prevent excessive bone loss and to minimize bone damage. SREBP2 is a key transcription factor for cholesterol biosynthesis and a sensor for intracellular lipids. However, how the crosstalk between SREBP2 and lipid metabolism contributes to osteoclasts has not been determined.
Read the full summary ↓
Here, we reveal that SREBP2 is a negative regulator of osteoclastogenesis. Targeted deletion of SREBP2 in myeloid cells result in low bone mass and accelerates inflammatory bone destruction. SREBP2-mediated regulation of osteoclastogenesis is independent of its canonical function in cholesterol biosynthesis but is mediated, in part, by its downstream target, interferon regulatory factor (IRF)7. Taken together, our study highlights the SREBP2-IRF7 regulatory circuit forms as a negative feedback inhibitory loop in osteoclast differentiation that represents a novel mechanism to restrain deleterious pathological bone destruction.
Published in
SREBP2 restricts osteoclast differentiation and activity by regulating IRF7 and limits inflammatory bone erosion
Kim H, Choi IA, Umemoto A et al. · Bone research 2024 · PMID 39191742 · doi:10.1038/s41413-024-00354-4
This dataset
Open GSE172007 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 GSE172007_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 PRJNA721686 and SRA study SRP314696. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39191742) ↗
Study design
8 conditions, mostly in duplicate
SREBP2 deficient macrophages ×2 SREBP2 deficient macrophages stimulated with … ×2 LysM cre Control macrophages ×2 LysM cre Control macropahges stimulated with … ×2 IRF7 deficient macrophages ×2 IRF7 deficient macrophages stimulated with RA… ×2 C57BL6 Control macrophages ×2 C57BL6 Control macropahges stimulated with RA… ×2

Supports a case/control comparison: 4 samples read as cases, 4 as controls.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 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
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