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Chondroprotective functions of neutrophil-derived extracellular vesicles via promoting the production of secreted frizzled related protein 5 in cartilage

GSE271169 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/11/26 Platform GPL24676
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 × Control chondrocyte vs 3 × Chondrocyte stimulated by IL-1β alone vs 3 × Chondrocyte stimulated by IL-1β +non-stimulated neutrophil derived Evs vs 3 × Chondrocyte stimulated by IL-1β +TGF-β-stimulated neutrophil derived EvsGroups 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
Chondroprotective functions of neutrophil-derived extracellular vesicles by promoting the production of secreted frizzled-related protein 5 in cartilageCell communication and signaling : CCS · 2024
Summary (written by the submitters)
Neutrophil extracellular vesicles (EVs) are known to play a protective role in arthritic joints by suppressing inflammation and cartilage degeneration. In the current study, we investigated the functional characteristics of EVs derived from stimulated neutrophils and their protective effects in cartilage repair in vitro. We first optimized the stimulation conditions of neutrophils that led to production of EVs with chondroprotective function.
Read the full summary ↓
To understand this protective mechanism, EVs from TGF-β-stimulated neutrophils were added to stimulated chondrocytes with IL-1β, and their responses were examined by bulk-RNA analysis.
Published in
Chondroprotective functions of neutrophil-derived extracellular vesicles by promoting the production of secreted frizzled-related protein 5 in cartilage
Kitahara K, Ebata T, Liyile C et al. · Cell communication and signaling : CCS 2024 · PMID 39604981 · doi:10.1186/s12964-024-01953-8
This dataset
Open GSE271169 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 GSE271169_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 PRJNA1130388 and SRA study SRP517213. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39604981) ↗
Study design
3 × Control chondrocyte vs 3 × Chondrocyte stimulated by IL-1β alone vs 3 × Chondrocyte stimulated by IL-1β +non-stimulated neutrophil derived Evs vs 3 × Chondrocyte stimulated by IL-1β +TGF-β-stimulated neutrophil derived Evs

Supports a case/control comparison: 9 samples read as cases, 3 as controls.

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
Datasets on a similar topic

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