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iPSC-based modeling of preeclampsia identifies defects in extravillous trophoblast differentiation

GSE243579 Homo sapiens (human) RNA-seq (gene expression) 144 samples Submitted 2024/03/27 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 144 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
Homo sapiens (human)
Samples
144 samples: 48 conditions, mostly in triplicateGroups 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
iPSC-based modeling of preeclampsia identifies epigenetic defects in extravillous trophoblast differentiationiScience · 2024
Summary (written by the submitters)
Preeclampsia (PE) is a hypertensive pregnancy disorder with increased risk of maternal and fetal morbidity and mortality. Abnormal extravillous trophoblast (EVT) development and function is considered to be the underlying cause of PE, but has not previously been modeled in vitro. We previously derived induced pluripotent stem cells (iPSC) from placentas of PE patients and characterized abnormalities in formation of syncytiotrophoblast and responses to changes in oxygen tension.
Read the full summary ↓
In this study, we converted these primed iPSC to naïve iPSC, then derived trophoblast stem cells (TSC) and EVT to evaluate molecular mechanisms underlying PE. We found that primed (but not naïve) iPSC-derived PE-EVT have reduced surface HLA-G, blunted invasive capacity, and altered EVT-specific gene expression. These abnormalities correlated with promotor hypermethylation of genes associated with the epithelial-mesenchymal transition pathway, specifically in primed-iPSC derived PE-EVT. Our findings indicate that abnormal epigenetic regulation might play a role in the PE pathogenesis.
Published in
iPSC-based modeling of preeclampsia identifies epigenetic defects in extravillous trophoblast differentiation
Morey R, Bui T, Cheung VC et al. · iScience 2024 · PMID 38623329 · doi:10.1016/j.isci.2024.109569
This dataset
Open GSE243579 in finder → Find more human 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 GSE243579_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 PRJNA1018965 and SRA study SRP461841. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38623329) ↗
Study design
48 conditions, mostly in triplicate
Primary_1048_EVT ×3 Primary_1048_hTSC ×3 Primary_1049_EVT ×3 Primary_1049_hTSC ×3 Primary_1276C_EVT ×3 Primary_1276C_hTSC ×3 iPSC3_1754_Naive_EVT ×3 iPSC3_1754_Naive_hTSC ×3 +40 more

Supports a between-group comparison across 144 samples.

How we read this: 48 replicated groups read from 144 sample titles; they account for 144 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

+ 104 more — browse all 144 samples with per-sample file links →

Datasets on a similar topic

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