GEO series

Multiomic analysis reveals that polyamines alter G. vaginalis-induced cervicovaginal epithelial cell dysfunction

GSE311352 Homo sapiens (human) RNA-seq (gene expression) 72 samples Submitted 2026/01/26 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 72 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: 72 samples: 24 conditions, mostly in triplicateGroups 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: Multiomic analysis reveals that polyamines alter G. vaginalis-induced cervicovaginal epithelial cell dysfunctionResearch square · 2026

Summary (written by the submitters)

An anaerobe-dominant, Lactobacillus-deplete cervicovaginal microbiome is associated with adverse reproductive outcomes. Gardnerella vaginalis, a common cervicovaginal anaerobe, alters cervicovaginal epithelial cell function, resulting in inflammatory immune responses and epithelial barrier breakdown. Specific host-microbial mechanisms inducing this epithelial dysfunction remain unknown.

Read the full summary ↓

Here we show microbe-specific alterations in cervicovaginal epithelial cell metabolite profiles where G. vaginalis, but not Lactobacillus crispatus, increases polyamine biosynthesis. Pretreatment with polyamines (putrescine, spermidine and spermine) globally shifts G. vaginalis-induced transcriptomic profiles. Alterations in transcripts encoding enzymes responsible for polyamine synthesis and catabolism provides further evidence that G. vaginalis modifies polyamine biosynthesis. Additionally, polyamine-mediated transcriptomic changes include genes related to bacterial defense, inflammation, and epigenetic processes. Polyamines mitigate G. vaginalis-induced inflammatory responses through reduction of cytokines, chemokines, and matrix metalloproteinases. The ability of cervicovaginal metabolites to alter microbe-mediated changes in epithelial cell function suggests that metabolite-microbe interactions are critical mediators of epithelial defense against a Lactobacillus-deplete microbiota.

Published in

Multiomic analysis reveals that polyamines alter G. vaginalis-induced cervicovaginal epithelial cell dysfunction

Anton L, Kholod O, Phatate R et al. · Research square 2026 · PMID 42396481 · doi:10.21203/rs.3.rs-8552817/v1

This dataset

Open GSE311352 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 GSE311352_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 PRJNA1369202 and SRA study SRP648796. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42396481) ↗

Study design

24 conditions, mostly in triplicate

Ectocervical, NT, noGV, ×3 Vaginal, NT, noGV, ×3 Ectocervical, SPM, noGV, ×3 Endocervical, NT, noGV, ×3 Vaginal, SPM, noGV, ×3 Ectocervical, SPD, noGV, ×3 Endocervical, SPM, noGV, ×3 Vaginal, SPD, noGV, ×3 +16 more

Supports a between-group comparison across 72 samples.

How we read this: 24 replicated groups read from 72 sample titles; they account for 72 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

GSM9323939 Ectocervical, NT, noGV, replicate 1 Ectocervical, NT, noGV,
GSM9323940 Vaginal, NT, noGV, replicate 1 Vaginal, NT, noGV,
GSM9323941 Ectocervical, SPM, noGV, replicate 1 Ectocervical, SPM, noGV,
GSM9323942 Endocervical, NT, noGV, replicate 1 Endocervical, NT, noGV,
GSM9323943 Vaginal, SPM, noGV, replicate 1 Vaginal, SPM, noGV,
GSM9323944 Ectocervical, SPD, noGV, replicate 1 Ectocervical, SPD, noGV,
GSM9323945 Endocervical, SPM, noGV, replicate 1 Endocervical, SPM, noGV,
GSM9323946 Vaginal, SPD, noGV, replicate 1 Vaginal, SPD, noGV,
GSM9323947 Ectocervical, PUT, noGV, replicate 1 Ectocervical, PUT, noGV,
GSM9323948 Endocervical, SPD, noGV, replicate 1 Endocervical, SPD, noGV,
GSM9323949 Vaginal, PUT, noGV, replicate 1 Vaginal, PUT, noGV,
GSM9323950 Ectocervical, NT, GV, replicate 1 Ectocervical, NT, GV,
GSM9323951 Endocervical, PUT, noGV, replicate 1 Endocervical, PUT, noGV,
GSM9323952 Vaginal, NT, GV, replicate 1 Vaginal, NT, GV,
GSM9323953 Ectocervical, SPM, GV, replicate 1 Ectocervical, SPM, GV,
GSM9323954 Endocervical, NT, GV, replicate 1 Endocervical, NT, GV,
GSM9323955 Vaginal, SPM, GV, replicate 1 Vaginal, SPM, GV,
GSM9323956 Ectocervical, SPD, GV, replicate 1 Ectocervical, SPD, GV,
GSM9323957 Endocervical, SPM, GV, replicate 1 Endocervical, SPM, GV,
GSM9323958 Vaginal, SPD, GV, replicate 1 Vaginal, SPD, GV,
GSM9323959 Ectocervical, PUT, GV, replicate 1 Ectocervical, PUT, GV,
GSM9323960 Endocervical, SPD, GV, replicate 1 Endocervical, SPD, GV,
GSM9323961 Ectocervical, NT, noGV, replicate 2 Ectocervical, NT, noGV,
GSM9323962 Vaginal, NT, noGV, replicate 2 Vaginal, NT, noGV,
GSM9323963 Ectocervical, SPM, noGV, replicate 2 Ectocervical, SPM, noGV,
GSM9323964 Endocervical, NT, noGV, replicate 2 Endocervical, NT, noGV,
GSM9323965 Vaginal, SPM, noGV, replicate 2 Vaginal, SPM, noGV,
GSM9323966 Ectocervical, SPD, noGV, replicate 2 Ectocervical, SPD, noGV,
GSM9323967 Endocervical, SPM, noGV, replicate 2 Endocervical, SPM, noGV,
GSM9323968 Vaginal, SPD, noGV, replicate 2 Vaginal, SPD, noGV,
GSM9323969 Ectocervical, PUT, noGV, replicate 2 Ectocervical, PUT, noGV,
GSM9323970 Vaginal, PUT, GV, replicate 1 Vaginal, PUT, GV,
GSM9323971 Endocervical, PUT, GV, replicate 1 Endocervical, PUT, GV,
GSM9323972 Endocervical, SPD, noGV, replicate 2 Endocervical, SPD, noGV,
GSM9323973 Vaginal, PUT, noGV, replicate 2 Vaginal, PUT, noGV,
GSM9323974 Ectocervical, NT, GV, replicate 2 Ectocervical, NT, GV,
GSM9323975 Endocervical, PUT, noGV, replicate 2 Endocervical, PUT, noGV,
GSM9323976 Vaginal, NT, GV, replicate 2 Vaginal, NT, GV,
GSM9323977 Ectocervical, SPM, GV, replicate 2 Ectocervical, SPM, GV,
GSM9323978 Endocervical, NT, GV, replicate 2 Endocervical, NT, GV,

+ 32 more — browse all 72 samples with per-sample file links →

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