GEO series

Host-directed microRNA-based intervention against intracellular Staphylococcus aureus: High-throughput screening identifies miR-4430, miR-147a, and miR-1249-5p as multifunctional antimicrobial candidates

GSE318734 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/02/23 Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 3 × A549 SA C vs 3 × A549 SA 4430 vs 3 × A549 SA 147a vs 3 × A549 SA 1249-5pGroups 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: Host-directed microRNA-based intervention against intracellular Staphylococcus aureus: high-throughput screening identifies miR-4430, miR-147a, and miR-1249-5p as multifunctional antimicrobial candidatesFrontiers in cellular and infection microbiology · 2026

Summary (written by the submitters)

The intracellular persistence of Staphylococcus aureus represents a major therapeutic challenge, as it facilitates immune evasion and limits the efficacy of antibiotics with poor intracellular activity. Host-directed therapies based on microRNAs (miRNAs) offer a promising alternative to overcome these limitations. We performed a high-throughput screen of 2,469 human miRNA mimics in S.

Read the full summary ↓

aureus USA300–infected A549 epithelial cells, followed by network centrality–based prioritization and validation across multiple S. aureus strains and epithelial cell lines. This approach identified ten candidate miRNAs, among which miR-4430, miR-1249-5p, and miR-147a consistently reduced intracellular bacterial burden and improved host cell viability. Host transcriptomic profiling revealed distinct yet complementary mechanisms of action: miR-4430 enhanced innate immune responses, including STAT1- and PTAFR-associated signaling, whereas miR-1249-5p and miR-147a modulated extracellular matrix organization and integrin-mediated adhesion, thereby impairing bacterial entry. Collectively, these miRNAs impose convergent host-driven pressures that restrict intracellular S. aureus proliferation. Our findings highlight the therapeutic potential of miRNA-based host-directed interventions, which could be combined with conventional antibiotics to improve infection control and reduce the emergence of resistance.

Published in

Host-directed microRNA-based intervention against intracellular Staphylococcus aureus: high-throughput screening identifies miR-4430, miR-147a, and miR-1249-5p as multifunctional antimicrobial candidates

Castañera P, Llano-Verdeja J, Ferrero HÁ et al. · Frontiers in cellular and infection microbiology 2026 · PMID 41959566 · doi:10.3389/fcimb.2026.1772100

This dataset

Open GSE318734 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 GSE318734_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 PRJNA1419864 and SRA study SRP675283. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41959566) ↗

Study design

3 × A549 SA C vs 3 × A549 SA 4430 vs 3 × A549 SA 147a vs 3 × A549 SA 1249-5p

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM9501755 A549 SA C-_1 A549 SA C
GSM9501756 A549 SA C-_2 A549 SA C
GSM9501757 A549 SA C-_3 A549 SA C
GSM9501758 A549 SA 4430_1 A549 SA 4430
GSM9501759 A549 SA 4430_2 A549 SA 4430
GSM9501760 A549 SA 4430_3 A549 SA 4430
GSM9501761 A549 SA 147a_1 A549 SA 147a
GSM9501762 A549 SA 147a_2 A549 SA 147a
GSM9501763 A549 SA 147a_3 A549 SA 147a
GSM9501764 A549 SA 1249-5p_1 A549 SA 1249-5p
GSM9501765 A549 SA 1249-5p_2 A549 SA 1249-5p
GSM9501766 A549 SA 1249-5p_3 A549 SA 1249-5p

Datasets on a similar topic

GSE270928 Single-cell sequencing of full-length transcripts and T-cell receptors with automated high-throughput Smart-seq3 [HT SS3] 6415 samples shares high-throughput
GSE276869 High-throughput transcriptomics screening of mixtures of BPA alternatives reveal additive effects in vitro 672 samples shares high-throughput
GSE252117 High-throughput transcriptomics of water extracts detects reductions in biological activity with water treatment processes 510 samples shares high-throughput
GSE271332 High-Throughput Transcriptomics Toxicity Assessment of Eleven Data-Poor Bisphenol A Alternatives 286 samples shares high-throughput
GSE292777 Incorporating Metabolic Competence into High-Throughput Profiling Assays 192 samples shares high-throughput
GSE314863 Repertoire FLEX (REFLEX) Enables High-Throughput Multiomic scRNAseq with AIR Detection 127 samples shares high-throughput
GSE255889 Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product 110 samples shares high-throughput
GSE297342 Assessing the Effects of Silver Nanoparticles on ARPE-19 Cells via High-Throughput Phenotypic Profiling with the Cell Painting Assay. 88 samples shares high-throughput

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.