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Administration of the HMGB1 fragment suppresses expression of collagen-related genes

GSE247430 Mus musculus (mouse) Single-cell RNA-seq 24 samples Submitted 2024/09/09 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 24 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
24 samples: 8 × Pancreas, Healthy, CD45-, sample vs 8 × Pancreas, Saline, CD45-, sample vs 8 × Pancreas, Peptide, CD45-, sampleGroups 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
High-mobility group box 1 fragment ameliorates chronic pancreatitis induced by caerulein in miceJournal of gastroenterology · 2024
Summary (written by the submitters)
To analyze cell profiles in pancreatic tissue, single-cell RNA-seq of CD45-negative cells was performed using pancreatic tissue obtained in the eighth week after HMGB1 fragment injection was begun. After conventional quality check and filtering, we recovered pancreas cells from normal pancreas, control group pancreas, and HMGB1 group pancreas.
Read the full summary ↓
The UMAP plots depicted 11 distinct cell clusters from the three groups, PDGFRα＋ cells had the most significant number of clusters, which exhibited a high level of Col1α1 gene expression in the bubble plot.Compared with the control and HMGB1 groups, the distribution of the PDGFRα＋ cell cluster was skewed in the normal group. We focused on PDGFRα＋ cell clusters that secrete large amounts of collagen and extracellular matrix components, which are central to the pathogenesis of CP. Many genes were significantly expressed in contrasting ways, gene clusters that were upregulated in the control compared with the normal group were downregulated in the HMGB1 compared with the control group. In contrast, gene groups that were downregulated in the control compared with the normal group were upregulated in the HMGB1 compared with the control group. HMGB1 fragment exposure was associated with a shift in the gene expression pattern of CP toward that of the normal pancreas. Expression of Ccn2 and Ccn1 was upregulated in the control group compared with the normal group but downregulated in the HMGB1 group compared with the control group. Pten expression was downregulated in the control versus normal group but upregulated in the HMGB1 group compared with the controls. Extracellular matrix–related genes in the pancreas were altered with HMGB1 fragment administration.
Published in
High-mobility group box 1 fragment ameliorates chronic pancreatitis induced by caerulein in mice
Hokkoku D, Sasaki K, Kobayashi S et al. · Journal of gastroenterology 2024 · PMID 38727823 · doi:10.1007/s00535-024-02112-z
This dataset
Open GSE247430 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 GSE247430_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 PRJNA1037543 and SRA study SRP471108. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38727823) ↗
Study design
8 × Pancreas, Healthy, CD45-, sample vs 8 × Pancreas, Saline, CD45-, sample vs 8 × Pancreas, Peptide, CD45-, sample

Supports a between-group comparison across 24 samples.

How we read this: 3 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
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