GEO series

High-mobility group box1 peptide ameliorates bronchopulmonary dysplasia (BPD) via suppressing inflammation and fibrosis in a mouse model.

GSE181497 Mus musculus (mouse) Single-cell RNA-seq 3 samples Submitted 2024/11/12 Platform GPL30172

At a glance

Single-cell RNA-seq · mouse · 3 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 3 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.
Paper: High-mobility group box-1 peptide ameliorates bronchopulmonary dysplasia by suppressing inflammation and fibrosis in a mouse modelBiochemical and biophysical research communications · 2023

Summary (written by the submitters)

Previously, we have shown that a synthesized peptide originated from high mobility group box-1 protein (HMGB1) induces a regenerative cascade via activating endogenous mesenchymal stem cells in the body. Here, we have tested whether the HMGB1 peptide can ameliorate BPD related manifestations. In a mouse BPD model established by hyperoxia exposure, three shots of the HMGB1 peptide significantly improved the survival and lung function.

Read the full summary ↓

Single-cell RNA-seq analysis on the lung showed that an inflammatory signature in macrophages and a fibrotic signature in fibroblasts induced by hyperoxia exposure were significantly suppressed by the HMGB1 peptide. These changes in transcriptome were also confirmed at the protein level. Together, the HMGB1 peptide treatment prevented the progression of BPD by suppressing inflammation and fibrosis. Our data serve as a foundation to develop new effective therapies for BPD.

Published in

High-mobility group box-1 peptide ameliorates bronchopulmonary dysplasia by suppressing inflammation and fibrosis in a mouse model

Hara T, Shimbo T, Masuda T et al. · Biochemical and biophysical research communications 2023 · PMID 37329659 · doi:10.1016/j.bbrc.2023.06.032

This dataset

Open GSE181497 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 GSE181497_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA752215 and SRA study SRP331176. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37329659) ↗

Samples in this study

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+ 3 more — browse all 3 samples with per-sample file links →

Datasets on a similar topic

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GSE241079 Role of reducing Hmbox1 in cardiac ischemia/reperfusion injury 12 samples shares box1
GSE322753 M2 Macrophage-Derived Exosomes Ameliorate BPD by Inhibiting Ferroptosis via Suppression of the ZAKα-p38 Signaling Pathway 12 samples shares bpd
GSE207448 Obox1 deficiency induceds subfertility in female mice 4 samples shares box1
GSE271417 Hedgehog-interacting protein orchestrates alveologenesis and protects against BPD and emphysema by modulating hedgehog-IGF1 signaling axis 2 samples shares bpd
GSE261666 BPDCN MYB Fusions Regulate Cell Cycle Genes, Impair Differentiation and Induce Myeloid-Dendritic Cell Leukemia [HoxCutRun] 27 samples shares bpd

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