← BioTransfer GEO Dataset Finder
GEO series

Time-course Transcriptomics Reveals Impact of Treponema pallidum on Microvascular Endothelial Cell Function and Phenotype

GSE281329 Homo sapiens (human) RNA-seq (gene expression) 39 samples Submitted 2025/09/29 Platform GPL20795
At a glance

RNA-seq (gene expression) · human · 39 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
39 samples: 8 conditions, mostly with about 5 replicates eachGroups 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
Time-course Transcriptomics Reveals the Impact of Treponema pallidum on Microvascular Endothelial Cell Function and PhenotypebioRxiv : the preprint server for biology · 2025
Summary (written by the submitters)
Syphilis, caused by Treponema pallidum subsp. pallidum, is an urgent global public health threat. Syphilis vaccine development has been impeded by limited understanding of the molecular mechanisms that enable T. pallidum to establish and maintain infection. The vascular endothelium is critical for T. pallidum attachment, dissemination, and host immune response initiation; however, the molecular details of T.
Read the full summary ↓
pallidum-endothelial interactions are incompletely understood. To enhance understanding, we performed time-course transcriptomic profiling on T. pallidum-exposed brain microvascular endothelial cells. These analyses showed T. pallidum exposure alters pathways related to extracellular matrix, growth factors, integrins, and Rho GTPases. The induced transcriptional response was consistent with endothelial to mesenchymal transition, a key process involved in fetal development and vascular dysfunction. This study provides a comprehensive understanding of the molecular response of endothelial cells to T. pallidum and identifies the host pathways that may cause syphilis disease symptoms, information that could aid syphilis vaccine design.
Published in
Time-course Transcriptomics Reveals the Impact of Treponema pallidum on Microvascular Endothelial Cell Function and Phenotype
Waugh S, Goodyear MC, Gomez A et al. · bioRxiv : the preprint server for biology 2025 · PMID 40654963 · doi:10.1101/2025.05.04.651946
This dataset
Open GSE281329 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 GSE281329_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 PRJNA1183389 and SRA study SRP543843. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40654963) ↗
Study design
8 conditions, mostly with about 5 replicates each
hCMEC/d3 cells, 12 hours control exposure ×5 hCMEC/d3 cells, 24 hours control exposure ×5 hCMEC/d3 cells, 45 minutes control exposure ×5 hCMEC/d3 cells, 4 hours control exposure ×5 hCMEC/d3 cells, 12 hours T. pallidum exposure ×5 hCMEC/d3 cells, 24 hours T. pallidum exposure ×5 hCMEC/d3 cells, 4 hours T. pallidum exposure ×5 hCMEC/d3 cells, 45 minutes T. pallidum exposu… ×4

Supports a between-group comparison across 39 samples.

How we read this: 8 replicated groups read from 39 sample titles; they account for 39 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
Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.