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High Rates of Placental Inflammation in Samples Collected by the MOMI Consortium

GSE240306 Homo sapiens (human) Single-cell RNA-seq 56 samples Submitted 2024/10/31 Platform GPL20301
At a glance

Single-cell RNA-seq · human · 56 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
56 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)
OBJECTIVES: The Multi-Omics for Mothers and Infants (MOMI) consortium aims to improve birth outcomes. We analyzed full thickness placental samples (e.g., basal plate, placenta/chorionic villi and the chorionic plate) collected by the 5 MOMI sites: The Alliance for Maternal and Newborn Health Improvement (AMANHI) Bangladesh, AMANHI Pakistan, AMANHI Tanzania, The Global Alliance to Prevent Prematurity and Stillbirth (GAPPS) Bangladesh and GAPPS Zambia.
Read the full summary ↓
STUDY DESIGN. The teams collected biopsies from 294 preterm (gestation <37 weeks) and 291 term (gestation ≥37 weeks) births. They were formalin-fixed and paraffin embedded. Tissue sections from these samples were stained with hematoxylin and eosin and subjected to morphological analyses. Other placental biopsies (n = 35 preterm, 21 term) were collected in RNAlater, which enabled bulk transcriptomics. RESULTS. The morphological analyses revealed a surprisingly high rate of inflammation involving the basal plate, placenta/chorionic villi and the chorionic plate. The rate in chorionic villus samples ranged from 25% (Pakistan site) to 60% (Zambia site) of cases. Leukocyte infiltration in this location vs. the basal plate or chorion plate correlated with preterm birth. The transcriptomic analyses identified 267 genes as differentially expressed (DE) between placentas from preterm vs. term births (123 upregulated, 144 downregulated). Mapping the DE genes onto single cell RNA-seq data from human placentas suggested that all the component cell types, either singly or in subsets, contributed to the observed dysregulation. Consistent with the histopathological findings, (Gene Ontology) GO analyses highlighted leukocyte infiltration/activation and inflammatory responses in both the fetal and maternal compartments. CONCLUSION. Together these data suggested geographic- and/or population-based differences in placental inflammation and the triggers of preterm birth.
This dataset
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.

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 GSE240306_RAW.tar (it can run to tens of gigabytes).

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.

What the files usually look like: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1003120 and SRA study SRP453888. Searching any of these in the dataset finder brings you back here.

Samples in this study

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