GEO series

Effect of Col1a2 mutation in the gene expression of immature and mature osteoblasts in a mouse model of osteognesis imperfecta (OI)

GSE273779 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2024/08/25 Platform GPL17021

At a glance

RNA-seq (gene expression) · mouse · 14 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: 14 samples
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.

Summary (written by the submitters)

In Europe, approximately 85-90% of individuals with Osteogenesis Imperfecta (OI) have dominant pathogenic variants in the COL1A1 or COL1A2 genes whilst for Asian, especially Indian and Chinese cohorts, this ratio is much lower. This leads to decreased or abnormal Collagen type I production. Subsequently, bone formation is strongly reduced, causing bone fragility and liability to fractures throughout life.

Read the full summary ↓

OI is clinically classified in 5 types with the severity ranging from mild to lethal depending on the gene and the type and location of the OI-causative variant and the subsequent effect on (pro) collagen type I synthesis. However, the specific effects on the phenotype and function of osteoblasts are not fully understood. To investigate this, the OI murine model was used, with the oim/oim (OIM) mice closest resembling severely deforming OI type 3 in humans. We showed that in OIM, COL1 mutation results in a multifactorial inhibition of the osteogenic differentiation and maturation as well as inhibition of osteoclastogenesis. The phenotype of differentiated OIM osteoblasts also differs from that of wild type mature osteoblasts, with upregulated oxidative cell stress and autophagy pathways, possibly in response to the intracellular accumulation of type I collagen mRNA. The extracellular accumulation of defective type I collagen fibres contributes to activation of the TGF- signalling pathway and activates the inflammatory pathway. These effects combine to destabilise the balance of bone turnover, increasing bone fragility. Together, these findings identify the complex mechanisms underlying OI bone fragility in the OIM model of severe OI and can potentially enable identification of clinically relevant endpoints to assess the efficacy of innovative pro-osteogenic treatment for patients with OI.

This dataset

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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 GSE273779_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 PRJNA1143048. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 14 more — browse all 14 samples with per-sample file links →

Datasets on a similar topic

GSE270443 Osteoclast-independent osteocyte dendrite defects in mice bearing the Osteogenesis Imperfecta-causing Sp7 R342C mutation 12 samples shares imperfecta, mutation
GSE268601 The IFITM5 mutation in osteogenesis imperfecta type V is associated with an ERK/SOX9-dependent osteoprogenitor differentiation defect 6 samples shares imperfecta, mutation
GSE261776 Gene expression profile at single cell level of colorectal tumors from Col1a2-Cre/ERT2 and Col1a2-Cre/ERT2;TXNDC5fl/fl mice 4 samples shares col1a2
GSE286027 Next Generation Sequencing Facilitates Quantitative Analysis of Col1a2+ stromal cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice 6 samples shares col1a2
GSE286383 Next Generation Sequencing Facilitates Quantitative Analysis of Epithelial cells sorted from Col1a2-creERT;Bmpr1a and ctrl mice 6 samples shares col1a2
GSE333701 Transcriptional Profiling of Otic Capsule and Femur in the oim Mouse Model of Osteogenesis Imperfecta 140 samples shares imperfecta
GSE211533 mRNA expression in primary osteoblasts from wild-type and Fam102a knockout mice 6 samples shares osteoblasts
GSE291858 Expression profile of mRNA involved in glucocorticoid-induced apoptosis in osteoblasts 6 samples shares osteoblasts

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.