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Characterization of POP mixture redistribution and identification of their molecular signature in xenografted fat mice

GSE279353 Mus musculus (mouse) RNA-seq (gene expression) 54 samples Submitted 2025/04/16 Platform GPL34328
At a glance

RNA-seq (gene expression) · mouse · 54 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
54 samples: 9 conditions, mostly with about 6 replicates eachGroups 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
Characterization of POP mixture redistribution and identification of their molecular signature in xenografted fat miceEnvironmental pollution (Barking, Essex : 1987) · 2025
Summary (written by the submitters)
Persistent organic pollutants (POPs) are associated with many adverse health effects in humans, including cancers, immune, reproductive, neurological disorders and metabolic diseases. These chemicals are known to accumulate in fatty tissues, from which they can be released in other tissue compartments of living organisms, in particular, upon weight loss.
Read the full summary ↓
This dynamic distribution of POPs remains, however poorly investigated. In this study, a xenografted POP-contaminated adipose tissue (AT) model was used to assess 1) their concentrations in the ATs, the liver and the brain and 2) their associated effects by transcriptomics, metabolomics and lipidomics approaches. In the ATs, the liver and the brain of mice grafted with POP-contaminated fat pad, most of POPs were detected 3 days and 21 days after the graft with the highest concentrations in the ATs and the lowest concentrations in the brain. Conversely, per- and polyfluoroalkyl substances presented a distinct profile as they persist in the liver but not in the ATs or in the brain. In the AT of POP-exposed mice, the most dysregulated pathways were related to mitochondrial functions, endobiotic (carbohydrate, lipid, amino acid) and xenobiotic metabolism and inflammatory response. In the liver of grafted mice, many pathways related to mitochondrial functions and metabolism were dysregulated. These results support that realistic mixture of POPs that accumulate in AT and liver induces a systemic metabolic dysfunction which may represent the mechanisms by which the POPs can promote metabolic diseases such as obesity, type 2 diabetes and cardiovascular diseases.
Published in
Characterization of POP mixture redistribution and identification of their molecular signature in xenografted fat mice
Jamay T, Noirez P, Djemai H et al. · Environmental pollution (Barking, Essex : 1987) 2025 · PMID 40228731 · doi:10.1016/j.envpol.2025.126239
This dataset
Open GSE279353 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 GSE279353_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 PRJNA1172136 and SRA study SRP538161. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40228731) ↗
Study design
9 conditions, mostly with about 6 replicates each
eAT_Ctrl ×6 eAT_5X ×6 eAT_15X ×6 gliver_Ctrl ×6 gliver_5X ×6 gliver_15X ×6 geAT_Ctrl ×6 geAT_5X ×6 +1 more

Supports a between-group comparison across 54 samples.

How we read this: 9 replicated groups read from 54 sample titles; they account for 54 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

+ 14 more — browse all 54 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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