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Transcriptomic analysis delineates preterm prelabor rupture of membranes from preterm labor in preterm fetal membranes

GSE243831 Homo sapiens (human) RNA-seq (gene expression) 16 samples Submitted 2024/03/13 Platform GPL29480
At a glance

RNA-seq (gene expression) · human · 16 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
16 samples: 4 × preterm_labor_with_PPROM_amnion_tissue vs 4 × preterm_labor_with_PPROM_chorion_tissue vs 4 × preterm_labor_without_PPROM_amnion_tissue vs 4 × preterm_labor_without_PPROM_chorion_tissueGroups 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
Transcriptomic analysis delineates preterm prelabor rupture of membranes from preterm labor in preterm fetal membranesBMC medical genomics · 2024
Summary (written by the submitters)
We compared fetal membrane tissue from preterm labor deliveries to fetal tissue from preterm labor with preterm prelabor rupture of membranes (PPROM) deliveries to further explore the concept that spontaneous preterm birth can result from the initializing of two separate but overlapping pathological events. Chorioamnion, separated into amnion and chorion, was collected from gestationally age-matched cases and controls within 15 minutes of birth, and analyzed using RNA sequencing.
Read the full summary ↓
In our study, transcriptome analysis of preterm fetal membranes revealed distinct differentially expressed genes for PPROM, separate from preterm labor. This study is the first to report transcriptome data that reflects the individual pathophysiology of amnion and chorion tissue from PPROM deliveries.
Published in
Transcriptomic analysis delineates preterm prelabor rupture of membranes from preterm labor in preterm fetal membranes
Underhill LA, Mennella JM, Tollefson GA et al. · BMC medical genomics 2024 · PMID 38443884 · doi:10.1186/s12920-024-01841-7
This dataset
Open GSE243831 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 GSE243831_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 PRJNA1020124 and SRA study SRP462689. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38443884) ↗
Study design
4 × preterm_labor_with_PPROM_amnion_tissue vs 4 × preterm_labor_with_PPROM_chorion_tissue vs 4 × preterm_labor_without_PPROM_amnion_tissue vs 4 × preterm_labor_without_PPROM_chorion_tissue

Supports a between-group comparison across 16 samples.

How we read this: 4 replicated groups read from 16 sample titles; they account for 16 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
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