GEO series

PCB126 Modifies the Murine Hepatic Transcriptome and Metallome to Promote Alcohol-associated Liver Disease Pathogenesis

GSE244388 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/05/01 Platform GPL30172

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: 24 samples, each with a distinct title — no replicated groupsGroups 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: Multiomics Analysis of PCB126's Effect on a Mouse Chronic-Binge Alcohol Feeding ModelEnvironmental health perspectives · 2024

Summary (written by the submitters)

Background: Environmental pollutants, including polychlorinated biphenyls (PCBs) have been shown to alter and promote the development of alcohol-associated liver disease (ALD). Our group recently demonstrated that PCB126 promoted steatosis, hepatomegaly, and modulated intermediary metabolism in an ALD rodent model. Objectives: To better understand how PCB126 promoted ALD, the current study adopts transcriptomic and metallomic approaches to identify mechanistic pathways involved in this promotion.

Read the full summary ↓

Methods: Briefly, male C57BL/6J mice were exposed to 0.2 mg/kg PCB126 or corn oil vehicle prior to ethanol feeding in the chronic-binge model. Liver tissues were collected for RNA sequencing and ICP-MS metals quantification. Results: PCB126 uniquely modified the transcriptome in EtOH-fed mice in terms of variance. EtOH feeding alone resulting in >4000 differentially expressed genes (DEGs) and PCB126 exposure resulted in more DEGs in the EtOH-fed group over the pair-fed group. Top gene ontology (GO) biological processes indicated ‘peptidyl tyrosine modifications’ and GO molecular function processes showed a loss of ‘metal, and ion, and zinc binding’. Western blot analysis depicted that the JAK2-STAT5 signaling axis was disrupted by the enhanced loss of phosphorylated JAK2 in EtOH+PCB126 mice. Quantified liver essential metal levels were overall depleted by EtOH feeding, and potassium, magnesium, cobalt, and zinc were further decreased by PCB126. Discussion: The results suggests that phosphorylation and metal binding are disrupted in EtOH+PCB126 mice, implying that evolutionarily conserved homeostatic signaling mechanisms are modified by pollutant exposure in EtOH-fed mice. The loss of phosphorylation and essential metals are two suggestive modes of action that may explain the promotion of disease by PCB126 in ALD.

Published in

Multiomics Analysis of PCB126's Effect on a Mouse Chronic-Binge Alcohol Feeding Model

Gripshover TC, Wahlang B, Head KZ et al. · Environmental health perspectives 2024 · PMID 38619879 · doi:10.1289/EHP14132

This dataset

Open GSE244388 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 GSE244388_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 PRJNA1022507 and SRA study SRP463942. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38619879) ↗

Study design

24 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 24 sample titles: 24 distinct titles with little repetition. 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

GSM7814595 [Liver] [Pair-fed + Vehicle] [Replicate 1]
GSM7814596 [Liver] [Pair-fed + Vehicle] [Replicate 2]
GSM7814597 [Liver] [Pair-fed + Vehicle] [Replicate 3]
GSM7814598 [Liver] [Pair-fed + Vehicle] [Replicate 4]
GSM7814599 [Liver] [Pair-fed + Vehicle] [Replicate 5]
GSM7814600 [Liver] [Pair-fed + Vehicle] [Replicate 6]
GSM7814601 [Liver] [Pair-fed + PCB 126] [Replicate 1]
GSM7814602 [Liver] [Pair-fed + PCB 126] [Replicate 2]
GSM7814603 [Liver] [Pair-fed + PCB 126] [Replicate 3]
GSM7814604 [Liver] [Pair-fed + PCB 126] [Replicate 4]
GSM7814605 [Liver] [Pair-fed + PCB 126] [Replicate 5]
GSM7814606 [Liver] [Pair-fed + PCB 126] [Replicate 6]
GSM7814607 [Liver] [Ethanol-fed + Vehicle] [Replicate 1]
GSM7814608 [Liver] [Ethanol-fed + Vehicle] [Replicate 2]
GSM7814609 [Liver] [Ethanol-fed + Vehicle] [Replicate 3]
GSM7814610 [Liver] [Ethanol-fed + Vehicle] [Replicate 4]
GSM7814611 [Liver] [Ethanol-fed + Vehicle] [Replicate 5]
GSM7814612 [Liver] [Ethanol-fed + Vehicle] [Replicate 6]
GSM7814613 [Liver] [Ethanol-fed + PCB 126] [Replicate 1]
GSM7814614 [Liver] [Ethanol-fed + PCB 126] [Replicate 2]
GSM7814615 [Liver] [Ethanol-fed + PCB 126] [Replicate 3]
GSM7814616 [Liver] [Ethanol-fed + PCB 126] [Replicate 4]
GSM7814617 [Liver] [Ethanol-fed + PCB 126] [Replicate 5]
GSM7814618 [Liver] [Ethanol-fed + PCB 126] [Replicate 6]

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.