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The effect of G-MDSCs depletion on the gene expression profile of hepatocytes at different times following 70% hepatectomy

GSE277186 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2024/09/29 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 12 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
12 samples: 3 × Hepatocytes, control, POD1, vs 3 × Hepatocytes, control, POD2, vs 3 × Hepatocytes, G-MDSC depletion, POD1, vs 3 × Hepatocytes, G-MDSC depletion, POD2,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
Myeloid derived suppressor cells mediate hepatocyte proliferation and immune suppression during liver regeneration following resectionGenes and immunity · 2024
Summary (written by the submitters)
Liver regeneration following resection is a complex process relying on coordinated pathways and cell types in the remnant organ. Myeloid-Derived Suppressor Cells (MDSCs) have a role in liver regeneration-related angiogenesis but their influence on hepatocyte proliferation and immune modulation during liver regeneration is unclear. We examined the transcriptional response of regenerating liver hepatocytes after major resection in mice with CD11b+Ly6G+ MDSCs (G-MDSCs) depletion using RNA sequencing.
Read the full summary ↓
Global gene expression profiling of regenerating hepatocytes upon G-MDSC depletion revealed disrupted transcriptional progression from day one to day two after major liver resection. Key genes and pathways related to hepatocyte proliferation and immune response were differentially expressed upon MDSC depletion. This study provides evidence that MDSCs contribute to early liver regeneration by promoting hepatocyte proliferation and modulating the intra-liver immune response. These findings illuminate the multifaceted role of MDSCs in liver regeneration.
Published in
Myeloid derived suppressor cells mediate hepatocyte proliferation and immune suppression during liver regeneration following resection
Nachmany I, Nevo S, Edelheit S et al. · Genes and immunity 2024 · PMID 39488626 · doi:10.1038/s41435-024-00303-5
This dataset
Open GSE277186 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 GSE277186_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 PRJNA1161156 and SRA study SRP532730. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39488626) ↗
Study design
3 × Hepatocytes, control, POD1, vs 3 × Hepatocytes, control, POD2, vs 3 × Hepatocytes, G-MDSC depletion, POD1, vs 3 × Hepatocytes, G-MDSC depletion, POD2,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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