Small RNA-seq Analysis

ROSALIND's Small RNA-seq Analysis (Gene Regulation & Anti-Sense) is a cloud-based discovery platform designed to empower biologists and researchers to analyze, visualize, and interpret small RNA sequencing data — without requiring programming, bioinformatics expertise, or biostatistics knowledge. The platform is purpose-built for scientists working in Oncology, Immunology, Regenerative Medicine, Drug Discovery, and related fields who need to understand the role of miRNA and other small noncoding RNAs in gene regulation.

Small RNA sequencing (SmallRNA-Seq) leverages next-generation sequencing (NGS) technologies to characterize small noncoding RNA molecules between 20 and 200 nucleotides in length, including miRNA, snRNA, snoRNA, scRNA, piRNA, and siRNA. These molecules perform critical cellular functions such as RNAi, RNA processing and modification, gene silencing, epigenetic modifications, protein stability, and transport. ROSALIND provides basic analysis pipelines for all small RNA classes and expanded analysis and interpretation capabilities specifically for miRNAs, the most commonly studied class.

Analysis & Discovery Capabilities

• Analyze miRNA-seq data directly from FASTQ files or import processed counts data (raw or normalized)
• Record experiment design and custom biological attributes
• Import NCBI Short Read Archive public data with full support for NCBI BioProject and BioSample metadata models
• Capture metadata with NCBI BioSample attributes
• Perform covariate and batch corrections with differential comparisons
• Set up comparisons using biological attributes to minimize differential accessibility errors
• Create customizable gene filters to adjust fold change and p-value cut-off parameters
• Download publication-ready figures and interactive plots
• Explore pathway, disease, and drug knowledge bases
• Real-time collaboration and results sharing across teams and institutions
• Multi-omic analyses across experiment and assay types

Five Steps to Small RNA-Seq Data Analysis on ROSALIND

1. Experiment Design: Begin by creating a new experiment and capturing the experiment design through a guided experience that records biological objectives, sample attributes, and analysis parameters. ROSALIND supports NCBI BioProject and BioSample models and allows scientists to define custom attributes. The platform accommodates both raw FASTQ files and processed counts data, and automatically calibrates analysis pipelines for a broad library of sample and library preparation kits, accounting for strandedness, strand direction, unique molecular identifiers (UMIs), trimming requirements, and adapters.
2. Quality Control: ROSALIND's Quality Control Intelligence automatically identifies and triages potential data quality issues before presenting results. Key QC metrics verified include Q30 scores, percentage of bases trimmed, read length before and after trimming, sample correlation, small RNA class distribution, and multidimensional scaling (MDS) or principal component analysis (PCA) for all samples.
3. Unlocking Results: After reviewing quality control, researchers unlock the experiment. ROSALIND calculates the required Analysis Units (AU) — generally 1 AU per single-sample FASTQ file for small RNA-seq experiments — with account balances and acquisition links accessible directly from the unlock screen.
4. Analysis & Discovery: ROSALIND provides a comprehensive dashboard for differential expression and interpretation of small RNA-seq data. Differentially expressed miRNAs are presented with default filter settings of 1.5-fold change (up and down) and a p-Adjust of 0.05, with unlimited customizable filters available. The platform features deep interpretation of predicted and validated miRNA targets, associated diseases and drugs, and rich interactive visualizations including customizable heatmaps, volcano plots, MA plots, box plots, and bar plots. New comparisons can be added at any time, and miRNA secondary structures can be displayed alongside detailed per-miRNA information.
5. Collaboration & Data Sharing: ROSALIND Spaces are virtual data rooms enabling true scientist-to-scientist collaboration, allowing teams and external collaborators anywhere in the world to interactively explore shared experiments in real time — similar to working with Google Docs. Participants can add experiments, explore pathways, change cut-offs, add meta-analyses, and create new comparisons within the shared environment, with real-time activity feeds and historical reports.

Platform Highlights

• Designed for Scientists: No programming, bioinformatics, or biostatistics knowledge required; intuitive interface enables rapid onboarding with minimal training
• Powerful Analysis: Supports advanced capabilities including contamination detection, covariate correction, batch correction, and multi-omic analyses
• Rich Data Visualization: High-quality, publication-ready, interactive diagrams and plots including heatmaps, volcano plots, MA plots, and secondary structure displays
• Trusted Built-in Pipelines: Industry-standard, widely published bioinformatics tools tuned for accuracy and reproducibility
• Flexible Data Input: Accepts raw FASTQ files or processed counts (raw or normalized) from any source
• Security and Encryption: All communications and data transfers are encrypted, with multiple layers of data protection ensuring availability

ROSALIND is a cloud platform accessible via subscription for Pharma, Biotech, and Academic researchers, as well as Service Providers, Contract Research Organizations (CROs), and Academic Core Labs. API integration is available to enable programmatic addition of experiments to collaborative Spaces, and all users can join a Space with a free ROSALIND account.