← BioTransfer GEO Dataset Finder
GEO series

RNY1 partitions into extracellular vesicles and ribonucleoprotein particles and regulates macrophage programming by airway fluids during inflammation.

GSE333855 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2026/06/22 Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 20 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
20 samples: 5 conditions, mostly with about 4 replicates eachGroups 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)
YRNAs are small noncoding RNAs that are abundant in the extracellular space. Prior research has shown that YRNAs are present in most biofluids and that their levels fluctuate during disease. Yet our understanding of YRNA dynamics in the context of biofluid extracellular particles during disease processes is limited. In this study, we found that RNY1, one of two murine YRNAs, increases in airway fluid during allergen-induced lung inflammation and correlates with neutrophil infiltration.
Read the full summary ↓
Using RNase sensitivity assays and size exclusion chromatography, we determined that airway fluid RNY1 is protected by both EVs and protein-containing structures in distinct extracellular compartments. In contrast the other murine YRNA, RNY3, is only enriched in BALF EVs, suggesting that RNY1 is uniquely partitioned in heterogenous extracellular particles. Both EV-enriched and protein-enriched RNY1-containing extracellular compartments were able program robust pro-inflammatory transcriptional responses in target macrophages. RNY1 contributed to this programming, as macrophages treated with a protein-enriched compartment isolated from RNY1-/- mice demonstrated lower induction of interferon-associated genes. Together, this study demonstrates that YRNAs are heterogeneously packaged in complex biofluids and contribute to intercellular signaling axes during inflammation.
This dataset
Open GSE333855 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 GSE333855_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 PRJNA1472694 and SRA study SRP704991. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
5 conditions, mostly with about 4 replicates each
BMDM_PBS ×4 BMDM_RNY1+/+ EVFx ×4 BMDM_RNY1-/- EVFx ×4 BMDM_RNY1+/+ ProteinFx ×4 BMDM_RNY1-/- ProteinFx ×4

Supports a between-group comparison across 20 samples.

How we read this: 5 replicated groups read from 20 sample titles; they account for 20 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

Search all mouse 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.