GEO series

Obesogenic diet in mice leads to inflammation and oxidative stress in the mother in association with sex-specific changes in fetal development, inflammatory markers and placental transcriptome

GSE262011 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/05/01 Platform GPL24247

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: Obesogenic Diet in Mice Leads to Inflammation and Oxidative Stress in the Mother in Association with Sex-Specific Changes in Fetal Development, Inflammatory Markers and Placental TranscriptomeAntioxidants (Basel, Switzerland) · 2024

Summary (written by the submitters)

Obesity during pregnancy is related to adverse maternal and neonatal outcomes. Factors involved in these outcomes may include increased maternal insulin resistance, inflammation, oxidative stress and nutrient mishandling. The placenta is the primary determinant of fetal outcomes, and its function can be impacted by maternal obesity. The aim of this study in mice was to determine the effect of obesity on maternal lipid handling, inflammatory and redox state, and placental oxidative stress, inflammatory signalling, and gene expression relative to female and male fetal growth.

Read the full summary ↓

Here we showed that HFHS diet induced, in the dams, hepatic steatosis, oxidative stress (reduced catalase, elevated protein oxidation) and activation of pro-inflammatory pathways (p38-MAPK) along with imbalanced circulating cytokine concentrations (increased IL-6 and decreased IL-5 and IL-17A). HFHS fetuses were asymmetrically growth-restricted, showing sex-specific changes in circulating cytokines (GM-CSF, TNF-a, IL-6 and IFN-g). Morphology of the placenta Lz was modified by a HFHS diet, in association with sex-specific alterations in the expression of genes and proteins implicated in oxidative stress, inflammation, and stress signalling. Placental gene expression changes were comparable to that seen in models of intrauterine inflammation and were related to a transcriptional network involving transcription factors, LYL1 and PLAG1. In summary, this study shows that fetal growth restriction with maternal obesity is related to elevated oxidative stress, inflammatory pathways, and sex-specific placental changes. Our data are important given the marked consequences and the rising rates of obesity worldwide.

Published in

Obesogenic Diet in Mice Leads to Inflammation and Oxidative Stress in the Mother in Association with Sex-Specific Changes in Fetal Development, Inflammatory Markers and Placental Transcriptome

Candia AA, Lean SC, Zhang CXW et al. · Antioxidants (Basel, Switzerland) 2024 · PMID 38671859 · doi:10.3390/antiox13040411

This dataset

Open GSE262011 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 GSE262011_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 PRJNA1090037 and SRA study SRP496652. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38671859) ↗

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

GSM8155969 Placental labyrinth zone Ctrl_F_4075_01
GSM8155970 Placental labyrinth zone Ctrl_F_4085_02
GSM8155971 Placental labyrinth zone Ctrl_F_4091_03
GSM8155972 Placental labyrinth zone Ctrl_F_4061_04
GSM8155973 Placental labyrinth zone Ctrl_F_4126_05
GSM8155974 Placental labyrinth zone Ctrl_F_4154_06
GSM8155975 Placental labyrinth zone Ctrl_M_4075_07
GSM8155976 Placental labyrinth zone Ctrl_M_4085_08
GSM8155977 Placental labyrinth zone Ctrl_M_4091_09
GSM8155978 Placental labyrinth zone Ctrl_M_4061_10
GSM8155979 Placental labyrinth zone Ctrl_M_4154_11
GSM8155980 Placental labyrinth zone HFHS_F_3996_01
GSM8155981 Placental labyrinth zone HFHS_F_4062_02
GSM8155982 Placental labyrinth zone HFHS_F_4068_03
GSM8155983 Placental labyrinth zone HFHS_F_4073_04
GSM8155984 Placental labyrinth zone HFHS_F_4140_05
GSM8155985 Placental labyrinth zone HFHS_F_4177_06
GSM8155986 Placental labyrinth zone HFHS_M_3996_07
GSM8155987 Placental labyrinth zone HFHS_M_4062_08
GSM8155988 Placental labyrinth zone HFHS_M_4068_09
GSM8155989 Placental labyrinth zone HFHS_M_4073_10
GSM8155990 Placental labyrinth zone HFHS_M_4140_11
GSM8155991 Placental labyrinth zone HFHS_M_4177_12
GSM8155992 Placental labyrinth zone Ctrl_M_4126_12

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Search all mouse RNA-seq datasets in GEO →

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