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Long-read isoform sequencing reveals Aroclor1260-induced isoform expression in mouse liver

GSE308889 Mus musculus (mouse) RNA-seq (gene expression) 12 samples Submitted 2026/03/03 Platform GPL34585
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: 4 × Liver DMSO Control, vs 4 × Liver low NAFLD Activity Score + Ar1260 exposure, vs 4 × Liver high NAFLD Activity Score + Ar1260 exposure,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
Long-Read Isoform Sequencing Reveals Aroclor1260-Induced Isoform Usage in Mouse LiversGenes · 2026
Summary (written by the submitters)
Long-term exposure to polychlorinated biphenyls (PCBs) including the mixture of PCBs in Aroclor1260 (Ar1260) results in metabolic dysfunction-associated steatotic liver disease (MASLD) in mice and humans. Previously, we reported that chronic (34 wks.) exposure of normal low fat diet (LFD)-fed male mice to Ar1260 resulted in twelve hepatic RNA modifications.
Read the full summary ↓
We confirmed the downregulation NRF2 (Nfe2l2) network pathway associated with human liver diseases. Proteomic analysis of these same liver samples identified Ar1260 exposure-associated changes in protein abundance including altered selenoproteins: GPX4 and SELENBP2 were increased and SELENOS and SELENOF were reduced. Alternative splicing (AS) has been implicated in MASLD. Here we used long-read isoform sequencing (IsoSeq) to and differential transcript usage (DTU) to specific DTU gene differences depending on the severity of liver injury with Ar1260.
Published in
Long-Read Isoform Sequencing Reveals Aroclor1260-Induced Isoform Usage in Mouse Livers
Petri BJ, Piell KM, Wahlang B et al. · Genes 2026 · PMID 41751510 · doi:10.3390/genes17020126
This dataset
Open GSE308889 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 GSE308889_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 PRJNA1333336 and SRA study SRP625471. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41751510) ↗
Study design
4 × Liver DMSO Control, vs 4 × Liver low NAFLD Activity Score + Ar1260 exposure, vs 4 × Liver high NAFLD Activity Score + Ar1260 exposure,

Supports a between-group comparison across 12 samples.

How we read this: 3 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
Datasets on a similar topic

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