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Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [RNA-seq]

GSE225317 Mus musculus (mouse) RNA-seq (gene expression) 110 samples Submitted 2024/04/24 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 110 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
110 samples: 24 conditions, mostly with about 5 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
Trophectoderm biopsy of blastocysts following IVF and embryo culture increases epigenetic dysregulation in a mouse modelHuman reproduction (Oxford, England) · 2024
Summary (written by the submitters)
Trophectoderm biopsy for preimplantation genetic testing (TEBx) impacts placental and embryonic health during early development, with some alterations resolving while others worsening later in development. We observed that at E12.5, IVF + TEBx had a worse outcome in terms of changes in DNA methylation and differential gene expression in placentas and whole embryos compared with IVF alone.
Read the full summary ↓
These changes were reflected in alterations in placental morphology and blood vessel density. At E18.5, early changes in embryos were maintained or worsened, while molecular and morphological changes in the placenta were not different from the IVF group, except for changes in blood vessel density, which persisted. Of note is that most differences were sex specific. We conclude that TEBx has more detrimental effects in both mid-gestation placental and embryonic tissues, with changes in embryonic tissues persisting or worsening in later developmental stages compared to IVF alone. Additionally, consistent with previous work, we report sex differences in the observed effects. Finally, we identified that the addition of vitrification after TEBx has a more pronounced detrimental effect on placental and fetal health. Our findings provide additional support that more studies should be done to assess the impact of new procedures during ART to ensure healthy pregnancies and offspring outcomes.
Published in
Trophectoderm biopsy of blastocysts following IVF and embryo culture increases epigenetic dysregulation in a mouse model
Rhon-Calderon EA, Hemphill CN, Vrooman LA et al. · Human reproduction (Oxford, England) 2024 · PMID 37994669 · doi:10.1093/humrep/dead238
This dataset
Open GSE225317 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 GSE225317_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 PRJNA934960 and SRA study SRP422597. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37994669) ↗
Study design
24 conditions, mostly with about 5 replicates each
RNA library from E12.5 Female IVF Whole Fetus ×6 RNA library from E18.5 Female IVF+TEBx Placen… ×6 RNA library from E12.5 Female IVF Placenta ×5 RNA library from E12.5 Male IVF Placenta ×5 RNA library from E12.5 Male IVF+TEBx Placenta ×5 RNA library from E12.5 Female IVF+TEBx Whole … ×5 RNA library from E12.5 Female Natural Whole F… ×5 RNA library from E12.5 Male IVF+TEBx Whole Fe… ×5 +16 more

Supports a between-group comparison across 110 samples.

How we read this: 24 replicated groups read from 110 sample titles; they account for 110 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

+ 70 more — browse all 110 samples with per-sample file links →

Datasets on a similar topic

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