GEO series

Umbilical Cord Blood Cell Transcriptional and Methylation Signatures at Birth Are Associated with BPD Development [RNA-Seq]

GSE302178 Homo sapiens (human) DNA methylation 27 samples Submitted 2026/05/18 Platform GPL30173

At a glance

DNA methylation · human · 27 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 27 samples: 27 samples, each with a distinct title — no replicated groupsGroups 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: Umbilical cord blood cell transcriptional and methylation signatures at birth are associated with BPD development and chorioamnionitis: a pilot studyScientific reports · 2026

Summary (written by the submitters)

Bronchopulmonary dysplasia (BPD) is the most common respiratory disease in preterm infants born at less than 28 weeks gestation. Most existing clinical prediction models for BPD show limited accuracy in predicting BPD development when validated using external data, stressing the need for novel biomarkers to identify at-risk infants for early and effective interventions.

Read the full summary ↓

We leveraged existing frozen umbilical cord blood samples from the Northwestern University Cord Blood Biobank (NUCord) to perform parallel transcriptional and DNA methylation profiling. Chorioamnionitis-associated differentially expressed genes (DEGs) in our cohort included markers previously established in clinical and animal BPD studies, such as genes related to NF-κB signaling and immune responses. Importantly, these genes were highly associated with chorioamnionitis infection status specifically in preterm infants. We also identified that BPD development is associated with disrupted methylation signatures in microRNA genes and genes associated with glucose metabolism. Our results suggest that BPD development and chorioamnionitis are associated with distinct transcriptomic and epigenetic signatures when compared with healthy term and preterm infants. These signatures may represent biomarkers measurable at birth that predict BPD development during a time window when preventative or therapeutic interventions could be applied.

Published in

Umbilical cord blood cell transcriptional and methylation signatures at birth are associated with BPD development and chorioamnionitis: a pilot study

Liu Q, Helmin KA, Bailey JC et al. · Scientific reports 2026 · PMID 42141015 · doi:10.1038/s41598-026-53235-7

This dataset

Open GSE302178 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 GSE302178_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 PRJNA1289152. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42141015) ↗

Study design

27 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 27 sample titles: 27 distinct titles with little repetition. 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

GSM9097650 BPD-c1 (rnaseq)
GSM9097651 BPD-c2 (rnaseq)
GSM9097652 BPD-c3 (rnaseq)
GSM9097653 BPD-c4 (rnaseq)
GSM9097654 BPD-c5 (rnaseq)
GSM9097655 BPD1 (rnaseq)
GSM9097656 BPD2 (rnaseq)
GSM9097657 BPD3 (rnaseq)
GSM9097658 Preterm-c1 (rnaseq)
GSM9097659 Preterm-c2 (rnaseq)
GSM9097660 Preterm-c3 (rnaseq)
GSM9097661 Preterm-c4 (rnaseq)
GSM9097662 Preterm1 (rnaseq)
GSM9097663 Preterm2 (rnaseq)
GSM9097664 Preterm3 (rnaseq)
GSM9097665 Preterm4 (rnaseq)
GSM9097666 Term-c2 (rnaseq)
GSM9097667 Term-c3 (rnaseq)
GSM9097668 Term-c4 (rnaseq)
GSM9097669 Term-c5 (rnaseq)
GSM9097670 Term-c6 (rnaseq)
GSM9097671 Term-c7 (rnaseq)
GSM9097673 Term2 (rnaseq)
GSM9643512 Term3 (rnaseq)
GSM9643513 Term4 (rnaseq)
GSM9643514 Term5 (rnaseq)
GSM9643515 Term6 (rnaseq)

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