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Transcriptional changes upon overexpression of seven candidate miRNAs in human saphenous vein smooth muscle cells. [HSVSMC]

GSE253003 Homo sapiens (human) RNA-seq (gene expression) 33 samples Submitted 2025/01/10 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 33 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
33 samples: 11 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
Functional screening identifies miRNAs with a novel function inhibiting vascular smooth muscle cell proliferationMolecular therapy : the journal of the American Society of Gene Therapy · 2025
Summary (written by the submitters)
Proliferation of vascular smooth muscle cells (vSMCs) following injury is a crucial factor contributing to pathological vascular remodelling. MicroRNAs (miRNAs) are powerful gene regulators and attractive therapeutics agents. Here, we aim to systemically identify and characterise miRNAs with therapeutic potential in targeting aberrant vSMC proliferation.
Read the full summary ↓
We performed a high-throughput in vitro screen using a library of 2042 human miRNA-mimics for their impact on VSMC proliferation and identified seven novel antiproliferative miRNAs i.e miR-1827, miR-4774-3p, miR-5681b, miR-449b-5p, miR-491-3p, miR-323a-3p, and miR-892b.Overexpression of these 7 miRNAs affects proliferation of vSMCs from different vascular beds. Focusing on vein graft failure, a condition in which miRNA based therapeutics can be applied to the graft ex-vivo, we showed that these miRNAs reduced human saphenous vein SMC (HSVSMC) proliferation without inducing apoptosis or senescence, and five of them also significantly decreased migration.We performed RNA sequencing on HSVSMC overexpressing each of these 7 miRNAs. This analysis showed that each miRNA overexpression affects a core cell cycle gene network. However, this effect is mediated by distinct miRNA targets.
Published in
Functional screening identifies miRNAs with a novel function inhibiting vascular smooth muscle cell proliferation
Rodor J, Klimi E, Brown SD et al. · Molecular therapy : the journal of the American Society of Gene Therapy 2025 · PMID 39736815 · doi:10.1016/j.ymthe.2024.12.037
This dataset
Open GSE253003 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 GSE253003_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 PRJNA1063639 and SRA study SRP483372. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39736815) ↗
Study design
11 conditions, mostly in triplicate
Quiescent HSVSMC ×3 HSVSMC treated with IL1a+PDGFBB ×3 Mock transfected HSVSMC treated with IL1a+PDG… ×3 miRCTRL transfected HSVSMC treated with IL1a+… ×3 miR-323a-3p transfected HSVSMC treated with I… ×3 miR-449b-5p transfected HSVSMC treated with I… ×3 miR-491-3p transfected HSVSMC treated with IL… ×3 miR-892b transfected HSVSMC treated with IL1a… ×3 +3 more

Supports a between-group comparison across 33 samples.

How we read this: 11 replicated groups read from 33 sample titles; they account for 33 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

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