--- title: Use Case: Reanalyzing Public RNA-seq Data of IL-17A-Induced Changes in Osteoarthritis Cell Models description: Reanalyzing public RNA-seq data on IL-17A-induced changes in osteoarthritis cell models using g.nome and OmicsPlayground for streamlined, no-code bioinformatics workflows. image: https://almaden.io/hubfs/AG%20Website%20Header%20Images%20(5).png --- " [![Almaden](https://almaden.io/hubfs/AlmadenLogo_H_White.svg)](https://almaden.io/) [CONTACT US](https://almaden.io/contact-us) ![Featured](https://almaden.io/hubfs/AG%20Website%20Header%20Images%20(5).png) # Use Case: Reanalyzing Public RNA-seq Data of IL-17A-Induced Changes in Osteoarthritis Cell Models April 16, 2025 Interleukin-17A (IL-17A) is increasingly recognized for its role in osteoarthritis (OA), contributing to inflammation and joint degeneration. A recent study investigates how IL-17A and related cytokines affect gene expression in primary human chondrocytes and synovial fibroblasts derived from patients with end-stage knee OA. Public access to this dataset offers a unique opportunity to reproduce and explore the findings using modern, no-code bioinformatics tools. This analysis demonstrates how[g.nome®](https://almaden.io/platform) from Almaden Genomics and [Omics Playground](https://bigomics.ch/omics-playground/) from BigOmics Analytics facilitate streamlined, reproducible RNA-seq reanalysis.   ## Dataset Overview: Cytokine Response in OA-Derived Cells The dataset originates from the publication titled *"Interleukin-17A causes osteoarthritis-like transcriptional changes in human osteoarthritis-derived chondrocytes and synovial fibroblasts in vitro"* ([GEO Accession: GSE171952](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE171952)). The study includes 48 RNA-seq samples representing two cell types—chondrocytes and synovial fibroblasts—isolated from six OA patients. Each cell type was treated with IL-17A, IL-17AF, IL-17F, or control medium, revealing cytokine-specific gene expression profiles relevant to OA pathophysiology.   ## Data Retrieval: Automated Import of Public RNA-seq FASTQs Using the SRA Run Selector and project accession number SRP314543, the associated SRR accession numbers are identified. These are compiled in a text file (SRR\_Acc\_List.txt) and uploaded to g.nome.   ![BigOmics - 1](https://almaden.io/hs-fs/hubfs/BigOmics%20-%201.png?width=2132&height=1375&name=BigOmics%20-%201.png)   Within the g.nome interface, the **Fetch Public FASTQs** workflow [automates the download and formatting process](https://almaden.io/platform/analyze). After pasting in the SRR IDs and specifying parameters (ftp method and rnaseq as the pipeline), the workflow generates a sample sheet formatted for use in downstream analysis. This step eliminates the need for manual file handling or scripting.   ![BigOmics - 2](https://almaden.io/hs-fs/hubfs/BigOmics%20-%202.png?width=400&height=247&name=BigOmics%20-%202.png) ![BigOmics - 3](https://almaden.io/hs-fs/hubfs/BigOmics%20-%203.png?width=400&height=237&name=BigOmics%20-%203.png) ## Preprocessing: Quality Control and Count Generation The [RNA-seq Preprocessing workflow](https://almaden.io/applications/bulk-rna-seq) is initiated using the sample sheet generated previously. The reference genome is set to GRCh38, and the pipeline executes standard preprocessing steps.   ![BigOmics - 4](https://almaden.io/hs-fs/hubfs/BigOmics%20-%204.png?width=2195&height=845&name=BigOmics%20-%204.png)   Output files include: - **multiqc\_report.html** – Aggregated quality metrics from FASTQC, Cutadapt, Picard, and STAR. - **merged.gene\_counts.csv** – Gene-level count data across all samples. - **template\_samples.csv** – A metadata template prefilled with sample identifiers, editable for downstream grouping and annotation. ![BigOmics - 5](https://almaden.io/hs-fs/hubfs/BigOmics%20-%205.png?width=2365&height=754&name=BigOmics%20-%205.png)   This automated preprocessing workflow ensures consistent data quality while enabling users to remain focused on biological interpretation rather than technical execution.   ## Downstream Analysis: Interactive Visualization with Omics Playground To begin tertiary analysis, the RNA-seq Analyze feature in g.nome is used. The organism is set to *Human*, and users upload both the merged count file and the annotated sample metadata (osteo\_samples.csv). Analysis is launched directly into Omics Playground. Within the Omics Playground interface, users select analysis parameters, including: - Normalization method - Group comparisons for differential expression - Optional enrichment, clustering, and biomarker analyses The resulting dashboard provides an interactive environment for exploring biological signals within the dataset—without requiring any coding or command-line tools.   ![BigOmics - 6](https://almaden.io/hs-fs/hubfs/BigOmics%20-%206.png?width=3157&height=658&name=BigOmics%20-%206.png)![BigOmics - 6](https://almaden.io/hs-fs/hubfs/BigOmics%20-%206.png?width=3157&height=658&name=BigOmics%20-%206.png) ## Conclusion: Reproducible, Accessible Bioinformatics Workflows This use case illustrates how publicly available data can be reanalyzed using modern platforms designed for reproducibility and accessibility. With g.nome and Omics Playground, complex RNA-seq pipelines are transformed into guided workflows with intuitive interfaces, enabling users to move efficiently from raw sequencing files to biological insight. To view the complete analysis and explore the results in more detail, visit the companion [blog post here](https://bigomics.ch/blog/osteoarthritis-like-transcriptional-changes-induced-by-il-17a/). ---   ## From Workflow to Visualization — Seamlessly With the power of g.nome and Omics Playground, turning your RNA-seq outputs into interactive, insight-rich visualizations has never been easier. No uploads. No configuration headaches. Just a few clicks. Click the “Analyze in Omics Playground” button directly from g.nome, and a guided pop-up experience walks you through the final steps of data preparation—right inside the platform. ![BigOmics - 8](https://almaden.io/hs-fs/hubfs/BigOmics%20-%208.png?width=300&height=71&name=BigOmics%20-%208.png) Step-by-step guidance includes: **1. Review Counts** Preview and confirm the expression matrix automatically generated from your workflow output.   ![BigOmics - 9](https://almaden.io/hs-fs/hubfs/BigOmics%20-%209.png?width=700&height=552&name=BigOmics%20-%209.png)   **2. Review Samples** Check sample names and ensure your metadata is correctly assigned.   ![](https://almaden.io/hs-fs/hubfs/image-png-Apr-14-2025-07-44-00-2767-PM.png?width=700&height=555&name=image-png-Apr-14-2025-07-44-00-2767-PM.png)   **3. Create Comparisons** Define the conditions you want to compare—or use the Auto-detect option to generate suggested groupings. ![](https://almaden.io/hs-fs/hubfs/image-png-Apr-14-2025-07-45-25-3535-PM.png?width=700&height=554&name=image-png-Apr-14-2025-07-45-25-3535-PM.png)   **4. QC & Batch Correction** Fine-tune your data quality with tools for normalization, outlier removal, batch-effect correction, and more. ![](https://almaden.io/hs-fs/hubfs/image-png-Apr-14-2025-07-45-45-4694-PM.png?width=700&height=555&name=image-png-Apr-14-2025-07-45-45-4694-PM.png)   **5. Compute** Name your dataset, add a description, and launch the final analysis. ![](https://almaden.io/hs-fs/hubfs/image-png-Apr-14-2025-07-46-09-3613-PM.png?width=700&height=553&name=image-png-Apr-14-2025-07-46-09-3613-PM.png) Once configured, Omics Playground opens instantly—ready with powerful, interactive visualizations including PCA plots, clustering, differential expression, gene set enrichment, and biomarker discovery. Learn more about [BigOmics](https://bigomics.ch/). [![Almaden](https://almaden.io/hubfs/AlmadenLogo_H_White.svg)](https://almaden.io/) Almaden Genomics accelerates scientific discovery for bioinformaticians and their teams through its intuitive and user-friendly g.nome platform. This visual workspace allows anyone from the team to drag and drop toolkits from a curated library, speeding pipeline development from months to minutes. Quick Links - [Home](https://almaden.io) - [Contact Us](https://almaden.io/contact-us) - [Privacy Policy](https://almaden.io/privacy-policy) - [Security](https://almaden.io/security) - [Acceptable Use Policy](https://almaden.io/acceptable-use-policy) Contact 1409 Botham Jean Blvd. Office 1500 Dallas, TX 75215 469-480-3865 Copyright 2026 Almaden Genomics, LLC. All Rights Reserved. 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