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Uterine injury during diestrus leads to embryo spacing defects and perturbations in the Cox-2 pathway in subsequent pregnancies

GSE198799 Mus musculus (mouse) RNA-seq (gene expression) 18 samples Submitted 2024/04/01 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 18 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
18 samples: 18 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
Uterine injury during diestrus leads to placental and embryonic defects in future pregnancies in mice†Biology of reproduction · 2024
Summary (written by the submitters)
Uterine injury from procedures such as Cesarean sections (C-sections) often have severe consequences on subsequent pregnancy outcomes, leading to disorders such as placenta previa, placenta accreta, and infertility. With rates of C-section at approximately 30% of deliveries in the US that are projected to continue to climb, an understanding of the mechanisms by which these pregnancy disorders arise and opportunities for intervention are sorely needed.
Read the full summary ↓
However, there are currently no animal models to date that comprehensively assess the consequences of uterine injury. Here we describe the first rodent model of uterine injury on subsequent in utero outcomes. We observed four distinct phenotypes: reduced implantation events, increased rates of resorption, embryo misspacing, and placenta accreta-like features of reduced decidua and expansion of invasive trophoblasts. We also show that the appearance of embryo misspacing depends entirely on the phase of estrous cycle at the time of injury, leading us to identify differences in uterine wound healing as a function of estrous. Using RNA-seq, we identified perturbations in the expression of components of the COX-2 pathway after recovery from injury, a pathway that has previously been demonstrated to play an important role in embryo spacing. Therefore, we demonstrate that uterine damage in our novel mouse model engenders many uterine changes, most notably perturbed expression of COX-2 pathway-related genes, that ultimately lead to numerous placental and embryonic developmental defects with parallels to human pregnancy disorders.
Published in
Uterine injury during diestrus leads to placental and embryonic defects in future pregnancies in mice†
Zhang ET, Wells KL, Bergman AJ et al. · Biology of reproduction 2024 · PMID 38206869 · doi:10.1093/biolre/ioae001
This dataset
Open GSE198799 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 GSE198799_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 PRJNA816902 and SRA study SRP364562. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38206869) ↗
Study design
18 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 18 sample titles: 18 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
Datasets on a similar topic

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