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A smooth muscle cell lncRNA controls angiogenesis in chronic limb-threatening ischemia through a miR-143-3p/HHIP signaling axis

GSE290218 Mus musculus (mouse) RNA-seq (gene expression) 21 samples Submitted 2025/03/01 Platform GPL17021
At a glance

RNA-seq (gene expression) · mouse · 21 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
Mus musculus (mouse)
Samples
21 samples: 6 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.
Summary (written by the submitters)
Peripheral artery disease (PAD), affecting over 200 million people globally, often advances to chronic limb-threatening ischemia (CLTI), resulting in severe complications such as limb amputation and heightened mortality. Despite the potential of therapeutic angiogenesis, the mechanisms of cell-cell communication and transcriptional changes driving PAD are not fully understood.
Read the full summary ↓
Profiling long non-coding RNAs (lncRNAs) from human gastrocnemius muscles of human subjects with or without CLTI revealed that a vascular smooth muscle cell (SMC)-enriched lncRNA CARMN was reduced with CLTI. This study explored the role of how SMC-driven regulation of angiogenesis in limb ischemia is conferred via a unique lncRNA-miRNA coupled signaling pathway.To investigate this interesting project, we perform three RNA-seq project. The first one was performed between hypoxia and normoxia VSMCs to mimic the HLI disease in patients. The second one was performed between CARMN KO SMC and CARMN WT SMC to find the potential downstream signaling pathway. The third one was about the RNA-seq of the gastro muscle obtained from CARMN KO and CARMN WT mice after HLI surgery.
This dataset
Open GSE290218 in finder → Find more mouse 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 GSE290218_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 PRJNA1226586 and SRA study SRP565517. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
6 conditions, mostly in triplicate
CARMNKO ×5 CARMNWT ×4 CARMNSMCKO ×3 CARMNSMCWT ×3 HypoxiaSMC ×3 NormoxiaSMC ×3

Supports a between-group comparison across 21 samples.

How we read this: 6 replicated groups read from 21 sample titles; they account for 21 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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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.