GEO series

Circular RNA profiling identifies circ5078 as a BMPR2-derived regulator of endothelial translation

GSE245117 Homo sapiens (human) RNA-seq (gene expression) 24 samples Submitted 2025/09/03 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 24 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: 24 samples: 8 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: Circular RNA Profiling Identifies circ5078 as a BMPR2-Derived Regulator of Endothelial Proliferation and Stress ResponsesArteriosclerosis, thrombosis, and vascular biology · 2025

Summary (written by the submitters)

Germline loss-of-function BMPR2 mutations are the leading genetic cause of pulmonary arterial hypertension (PAH) and are strongly linked to aberrant endothelial proliferation and impaired translational stress responses. While these effects are generally attributed to a loss of the type-II bone morphogenetic protein receptor (BMPR-II), we used circular RNA profiling to identify circ5078, a BMPR2-derived circular RNA that regulates endothelial translation and cellular phenotype.

Read the full summary ↓

circ5078 and linear BMPR2 mRNA exert opposing effects on endothelial proliferation and stress granule formation, while influencing the translational efficiency of multiple genes by regulating ribosome assembly and translational initiation. In PAH patient-derived endothelial cells lacking linear BMPR2 mRNA, circ5078 depletion rescued impaired translational stress responses by rebalancing circular to linear transcript levels, independent of BMPR-II protein. By identifying circ5078 as a functional BMPR2 gene product, this work reveals interdependent roles for both linear and circular BMPR2 transcripts as regulators endothelial translation and proliferation

Published in

Circular RNA Profiling Identifies circ5078 as a BMPR2-Derived Regulator of Endothelial Proliferation and Stress Responses

VandenBroek MM, Sharp MC, Thompson P et al. · Arteriosclerosis, thrombosis, and vascular biology 2025 · PMID 40772817 · doi:10.1161/ATVBAHA.124.322455

This dataset

Open GSE245117 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 GSE245117_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 PRJNA1026963 and SRA study SRP465808. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40772817) ↗

Study design

8 conditions, mostly in triplicate

siControl Input N ×3 siLinear Input N ×3 si5078 Input N ×3 siLinear+5078 Input N ×3 siControl Poly N ×3 siLinear Poly N ×3 si5078 Poly N ×3 siLinear+5078 Poly N ×3

Supports a between-group comparison across 24 samples.

How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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

GSM7836983 siControl Input N1 siControl Input N
GSM7836984 siLinear Input N1 siLinear Input N
GSM7836985 si5078 Input N1 si5078 Input N
GSM7836986 siLinear+5078 Input N1 siLinear+5078 Input N
GSM7836987 siControl Input N2 siControl Input N
GSM7836988 siLinear Input N2 siLinear Input N
GSM7836989 si5078 Input N2 si5078 Input N
GSM7836990 siLinear+5078 Input N2 siLinear+5078 Input N
GSM7836991 siControl Input N3 siControl Input N
GSM7836992 siLinear Input N3 siLinear Input N
GSM7836993 si5078 Input N3 si5078 Input N
GSM7836994 siLinear+5078 Input N3 siLinear+5078 Input N
GSM7836995 siControl Poly N1 siControl Poly N
GSM7836996 siLinear Poly N1 siLinear Poly N
GSM7836997 si5078 Poly N1 si5078 Poly N
GSM7836998 siLinear+5078 Poly N1 siLinear+5078 Poly N
GSM7836999 siControl Poly N2 siControl Poly N
GSM7837000 siLinear Poly N2 siLinear Poly N
GSM7837001 si5078 Poly N2 si5078 Poly N
GSM7837002 siLinear+5078 Poly N2 siLinear+5078 Poly N
GSM7837003 siControl Poly N3 siControl Poly N
GSM7837004 siLinear Poly N3 siLinear Poly N
GSM7837005 si5078 Poly N3 si5078 Poly N
GSM7837006 siLinear+5078 Poly N3 siLinear+5078 Poly N

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