GEO series

A long-term high fat diet induces differential gene expression changes in spatially distinct adipose tissues.

GSE269663 Mus musculus (mouse) RNA-seq (gene expression) 16 samples Submitted 2024/06/12 Platform GPL30172

At a glance

RNA-seq (gene expression) · mouse · 16 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: 16 samples: 4 × SAT, lean, vs 4 × SAT, obese, vs 4 × VAT, lean, vs 4 × VAT, obese,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.

Summary (written by the submitters)

The accumulation of visceral adipose tissue (VAT) is strongly associated with cardiovascular disease and diabetes. In contrast, individuals with increased subcutaneous adipose tissue (SAT) without corresponding increases in VAT are associated with a metabolic healthy obese phenotype. These observations implicate dysfunctional VAT as a driver of disease processes, warranting investigation into obesity-induced alterations of distinct adipose depots.

Read the full summary ↓

To determine the effects of obesity on adipose gene expression, mice were fed either a high fat or normal laboratory diet for 12-14 months. Mesenteric VAT and hindlimb SAT were isolated from four lean controls and four obese mice for bulk RNA- sequencing. AT from lean controls served as a reference to obesity-induced changes. The long-term high fat diet induced the expression of 169 and 814 unique genes in SAT and VAT, respectively. SAT from obese mice exhibited a total of 308 differentially expressed genes (164 upregulated, 144 downregulated). VAT from obese mice exhibited 690 differentially expressed genes (262 genes upregulated, 428 downregulated). KEGG pathway and GO analyses revealed that metabolic pathways were upregulated in SAT vs. downregulated in VAT while inflammatory signaling was upregulated in VAT. We next determined common genes that were differentially regulated between SAT and VAT in response to obesity and identified four genes that exhibited this profile: elovl6 and kcnj15 were upregulated in SAT/downregulated in VAT while trdn and hspb7 were downregulated in SAT/ upregulated in VAT. We propose that these genes in particular should be further pursued to determine their roles in SAT vs. VAT with obesity.

This dataset

Open GSE269663 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 GSE269663_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 PRJNA1123180 and SRA study SRP513419. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

4 × SAT, lean, vs 4 × SAT, obese, vs 4 × VAT, lean, vs 4 × VAT, obese,

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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

GSM8324323 SAT, lean, 1 SAT, lean,
GSM8324324 SAT, lean, 2 SAT, lean,
GSM8324325 SAT, lean, 3 SAT, lean,
GSM8324326 SAT, lean, 4 SAT, lean,
GSM8324327 SAT, obese, 1 SAT, obese,
GSM8324328 SAT, obese, 2 SAT, obese,
GSM8324329 SAT, obese, 3 SAT, obese,
GSM8324330 SAT, obese, 4 SAT, obese,
GSM8324331 VAT, lean, 1 VAT, lean,
GSM8324332 VAT, lean, 2 VAT, lean,
GSM8324333 VAT, lean, 3 VAT, lean,
GSM8324334 VAT, lean, 4 VAT, lean,
GSM8324335 VAT, obese, 1 VAT, obese,
GSM8324336 VAT, obese, 2 VAT, obese,
GSM8324337 VAT, obese, 3 VAT, obese,
GSM8324338 VAT, obese, 4 VAT, obese,

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