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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

GSE225318 Mus musculus (mouse) DNA methylation 158 samples Submitted 2024/04/24 Platform GPL31191Platform GPL24247
At a glance

DNA methylation · mouse · 158 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Mus musculus (mouse)
Samples
158 samples: 30 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
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
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 GSE225318 in finder → Find more mouse methylation 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 GSE225318_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: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA934952 and SRA study SRP422597. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 37994669) ↗
Study design
30 conditions, mostly with about 5 replicates each
E12.5 Female IVF Placenta ×8 E12.5 Female IVF+TEBx Placenta ×8 E12.5 Female Natural Placenta ×8 E12.5 Male IVF Placenta ×8 E12.5 Male IVF+TEBx Placenta ×8 E12.5 Male Natural Placenta ×8 RNA library from E12.5 Female IVF Whole Fetus ×6 RNA library from E18.5 Female IVF+TEBx Placen… ×6 +22 more

Supports a between-group comparison across 158 samples.

How we read this: 30 replicated groups read from 158 sample titles; they account for 158 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

+ 118 more — browse all 158 samples with per-sample file links →

Datasets on a similar topic

Search all mouse methylation datasets in GEO →

Share this dataset

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.