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The effect of 70% hepatectomy on G-MDSCs transcription profile at different time points

GSE278987 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/11/09 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 24 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
24 samples: 8 conditions, mostly in triplicateGroups 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
CD11b(+)Ly6G(+) myeloid-derived suppressor cells promote liver regeneration in a murine model of major hepatectomyFASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019
Summary (written by the submitters)
Liver regeneration depends on sequential activation of pathways and cells involving the remaining organ in recovery of mass. Proliferation of parenchyma is dependent on angiogenesis. Understanding liver regeneration-associated neovascularization may be useful for development of clinical interventions. Myeloid-derived suppressor cells (MDSCs) promote tumor angiogenesis and play a role in developmental processes that necessitate rapid vascularization.
Read the full summary ↓
We therefore hypothesized that the MDSCs could play a role in liver regeneration. Following partial hepatectomy, MDSCs were enriched within regenerating livers, and their depletion led to increased liver injury and postoperative mortality, reduced liver weights, decreased hepatic vascularization, reduced hepatocyte hypertrophy and proliferation, and aberrant liver function. Gene expression profiling of regenerating liver-derived MDSCs demonstrated a large-scale transcriptional response involving key pathways related to angiogenesis. Functionally, enhanced reactive oxygen species production and angiogenic capacities of regenerating liver-derived MDSCs were confirmed. A comparative analysis revealed that the transcriptional response of MDSCs during liver regeneration resembled that of peripheral blood MDSCs during progression of abdominal tumors, suggesting a common MDSC gene expression profile promoting angiogenesis. In summary, our study shows that MDSCs contribute to early stages of liver regeneration possibly by exerting proangiogenic functions using a unique transcriptional program.
Published in
CD11b(+)Ly6G(+) myeloid-derived suppressor cells promote liver regeneration in a murine model of major hepatectomy
Nachmany I, Bogoch Y, Sivan A et al. · FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2019 · PMID 30730772 · doi:10.1096/fj.201801733R
This dataset
Open GSE278987 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 GSE278987_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 PRJNA1169879 and SRA study SRP536986. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 30730772) ↗
Study design
8 conditions, mostly in triplicate
G-MDSCs, hepatectomy, POD1, ×3 G-MDSCs, hepatectomy, POD2, ×3 G-MDSCs, hepatectomy, POD3, ×3 G-MDSCs, hepatectomy, POD4, ×3 G-MDSCs, sham, POD1, ×3 G-MDSCs, sham, POD2, ×3 G-MDSCs, sham, POD3, ×3 G-MDSCs, sham, POD4, ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 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
Datasets on a similar topic

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