GEO series

Histopathologic and transcriptome profiling identify novel trophoblast lineage-specific defects in preeclampsia

GSE186257 Homo sapiens (human) RNA-seq (gene expression) 44 samples Submitted 2023/01/10 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 44 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: 44 samples
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.

Summary (written by the submitters)

Preeclampsia (PE) is a heterogeneous disease which lacks pathophysiology-based subclassification. Current clinical classification is based on gestational age at diagnosis and severity of disease. However, PE placentas have heterogeneous findings on pathologic exam. We combined clinical, pathological, immunohistochemical (IHC), and transcriptomic profiling to better subclassify this disease.

Read the full summary ↓

303 PE and 1388 non-hypertensive controls were included, with subgroups of samples used for each analysis. Detailed clinical and placental pathologic data were abstracted from our Obstetric Registry. Tissue studio (Definiens) was used for IHC analysis. RNAseq was performed using Illumina-NovaSeq using our standard pipeline. We found that maternal vascular malperfusion (MVM) in the placenta is associated with preterm PE and small-for-gestation neonates, with further subclassification into groups with and without fetal vascular malperfusion (FVM). Interestingly, MVM with FVM was further characterized by loss of proliferative cytotrophoblast, as confirmed by p63 IHC. Finally, transcriptomic analysis identified pathways associated with hypoxia and reduced cell-proliferation in PE-MVM placentas, and further subclassified this group into syncytiotrophoblast (STB)hi and extravillous trophoblast (EVT)hi PE, confirmed by IHC for trophoblast lineage-specific markers. Our findings suggest that PE can be subclassified based on underlying pathophysiologic changes, allowing identification of pathways which can be targeted for diagnostic and therapeutic purposes.

This dataset

Open GSE186257 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 GSE186257_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 PRJNA773083 and SRA study SRP342399. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 36853788) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 44 more — browse all 44 samples with per-sample file links →

Datasets on a similar topic

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GSE327405 USP22 Suppresses Trophoblast Cell Necroptosis in Preeclampsia by Stabilizing KAT2A-Mediated Histone Acetylation at the SFRP1 Promoter 12 samples shares preeclampsia, trophoblast
GSE255126 Activated PRDM1-CREBBP Axis Contributes to Apoptosis and Impaired Invasion of Trophoblasts: A Novel Mechanism Underlying Preeclampsia 10 samples shares preeclampsia, trophoblast
GSE306864 Placental transcriptome profiles in late-onset preeclampsia: a cross-sectional observational analysis stratified by fetal sex 58 samples shares preeclampsia
GSE272342 Transcriptomics profiling of singleton and twin placentas in the absence or presence of preeclampsia. 45 samples shares preeclampsia
GSE246536 Single-nucleus transcriptional profiling of the placenta reveals the syncytiotrophoblast stress response to COVID-19 17 samples shares trophoblast

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