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A cyclic peptide-grafted Fc with hepatocyte growth factor functionality ameliorates hepatic fibrosis in a non-alcoholic steatohepatitis mouse model.

GSE233051 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2024/07/04 Platform GPL28457
At a glance

RNA-seq (gene expression) · mouse · 36 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
36 samples: 10 × Liver, Control_HFD, vs 10 × Liver, Treated_HFD, vs 9 × Liver, Control_Standard_diet, vs 7 × Liver, Treated_Standard_diet,Groups 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
A cyclic peptide-grafted Fc with hepatocyte growth factor functionality ameliorates hepatic fibrosis in a non-alcoholic steatohepatitis mouse modeliScience · 2024
Summary (written by the submitters)
Although growth factors have significant therapeutic potential because of their regenerative functions, their poor pharmacokinetics and low stability hinder their therapeutic application. Nonalcoholic steatohepatitis (NASH) is characterized by lipid accumulation, inflammation, and fibrosis in the liver, which can progress to life-threatening conditions such as cirrhosis and liver cancer.
Read the full summary ↓
The hepatocyte growth factor (HGF)-Met receptor pathway has been proposed as a potential therapy for liver diseases including NASH due to its effects on liver regeneration, but the short half-life of recombinant HGF limits its clinical use. Here, we designed a Met agonist with a long half-life by grafting two Met-binding macrocyclic peptides into loops of the crystallizable region (Fc) of immunoglobulin. This surrogate Met agonist ameliorated liver fibrosis and inflammation in a mouse model of NASH, indicating its potential therapeutic use. This study provides a foundation to develop growth factor and cytokine mimetics and to expand their therapeutic applications.
Published in
A cyclic peptide-grafted Fc with hepatocyte growth factor functionality ameliorates hepatic fibrosis in a non-alcoholic steatohepatitis mouse model
Rojas-Chaverra NM, Imamura R, Sato H et al. · iScience 2024 · PMID 39108737 · doi:10.1016/j.isci.2024.110426
This dataset
Open GSE233051 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 GSE233051_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 PRJNA974837 and SRA study SRP438829. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39108737) ↗
Study design
10 × Liver, Control_HFD, vs 10 × Liver, Treated_HFD, vs 9 × Liver, Control_Standard_diet, vs 7 × Liver, Treated_Standard_diet,

Supports a case/control comparison: 17 samples read as cases, 19 as controls.

How we read this: 4 replicated groups read from 36 sample titles; they account for 36 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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