GEO series

Gastric mucosal transcriptomic responses to diet-induced obesity and calorie restriction in mice

GSE315851 Mus musculus (mouse) RNA-seq (gene expression) 14 samples Submitted 2026/06/03 Platform GPL34290

At a glance

RNA-seq (gene expression) · mouse · 14 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: 14 samples: 5 × GastricMucosa_DIO_biol vs 5 × GastricMucosa_CR_biol vs 4 × GastricMucosa_Lean_biolGroups 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.

Summary (written by the submitters)

The transcriptional landscape of the gastric mucosa during diet-induced obesity (DIO) and calorie restriction (CR) is largely unexplored. Here, we profiled gastric mucosal gene expression changes induced in mice by DIO and CR and investigated the physiological role of Decidual Protein Induced by Progesterone 1 (Depp1) using newly-generated Depp1-knockout (KO) mice.

Read the full summary ↓

RNA sequencing revealed that DIO predominantly induces a pro-inflammatory transcriptional signature, whereas CR upregulates genes involved in peptide transport and extracellular matrix organization and downregulates immunity-related genes. Among CR-induced genes, Depp1 showed the strongest positive correlation with ghrelin expression. qRT-PCR confirmed that Depp1 expression in the gastric mucosa was restricted to ghrelin cells and demonstrated that CR also induces Depp1 upregulation in other tissues, including kidney, lung, and liver. Hepatic Depp1 upregulation by CR was absent in ghrelin-KO mice. Notably, Depp1-knockout mice displayed normal metabolic and hormonal responses to CR, including the expected rise in circulating ghrelin. However, after 16 weeks of ad libitum high-fat diet feeding, male Depp1-KO mice exhibited greater increases in body weight, food intake, fat mass, and lean mass, as well as reduced glucose tolerance compared with wild-type littermates. These changes were accompanied by altered hepatic expression of the GHSR (ghrelin receptor) antagonist Leap2 and the gluconeogenic gene Pck1. Thus, while Depp1 is a CR-induced, ghrelin cell-regulated gene that modulates hepatic transcriptional responses, it is not required for short-term metabolic adaptation to CR. Instead, Depp1 plays a protective role against the full development of metabolic dysfunction during DIO through mechanisms that remain to be elucidated.

This dataset

Open GSE315851 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 GSE315851_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 PRJNA1399427 and SRA study SRP660433. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

5 × GastricMucosa_DIO_biol vs 5 × GastricMucosa_CR_biol vs 4 × GastricMucosa_Lean_biol

Supports a between-group comparison across 14 samples.

How we read this: 3 replicated groups read from 14 sample titles; they account for 14 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

GSM9438498 GastricMucosa_Lean_biol rep_1 GastricMucosa_Lean_biol
GSM9438499 GastricMucosa_Lean_biol rep_2 GastricMucosa_Lean_biol
GSM9438500 GastricMucosa_Lean_biol rep_3 GastricMucosa_Lean_biol
GSM9438501 GastricMucosa_Lean_biol rep_4 GastricMucosa_Lean_biol
GSM9438502 GastricMucosa_DIO_biol rep_1 GastricMucosa_DIO_biol
GSM9438503 GastricMucosa_DIO_biol rep_2 GastricMucosa_DIO_biol
GSM9438504 GastricMucosa_DIO_biol rep_3 GastricMucosa_DIO_biol
GSM9438505 GastricMucosa_DIO_biol rep_4 GastricMucosa_DIO_biol
GSM9438506 GastricMucosa_DIO_biol rep_5 GastricMucosa_DIO_biol
GSM9438507 GastricMucosa_CR_biol rep_1 GastricMucosa_CR_biol
GSM9438508 GastricMucosa_CR_biol rep_2 GastricMucosa_CR_biol
GSM9438509 GastricMucosa_CR_biol rep_3 GastricMucosa_CR_biol
GSM9438510 GastricMucosa_CR_biol rep_4 GastricMucosa_CR_biol
GSM9438511 GastricMucosa_CR_biol rep_5 GastricMucosa_CR_biol

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