ChIP-seq Analysis

ROSALIND's ChIP-seq Analysis for Histone Mark & Transcription Factor is a cloud-based discovery platform designed to help pharma, biotech, and academic researchers analyze protein interactions with DNA without requiring programming or bioinformatics expertise. By combining chromatin immunoprecipitation sequencing (ChIP-seq) methodology with an intuitive, interactive interface, ROSALIND enables scientists of every skill level to move from raw FASTQ files to deep biological insights — including differential binding, histone modifications, pathway exploration, and multi-omic analyses — all in a real-time collaborative environment.

ChIP-seq is a powerful method that combines chromatin immunoprecipitation with massively parallel DNA sequencing to identify binding sites of DNA-associated proteins such as transcription factors, polymerases, structural proteins, histone marks, and other chromatin-associated proteins. Understanding how these proteins interact with DNA to regulate gene expression is essential for fully characterizing biological processes and disease states, and this epigenetic information is complementary to genotype and expression analysis.

Analysis & Discovery Capabilities

• Analyze ChIP-seq data directly from raw FASTQ files
• Record experiment design and custom biological attributes
• Capture metadata using NCBI BioProject and BioSample models
• Perform covariate and batch corrections with differential binding comparisons
• Set up comparisons using biological attributes to minimize differential accessibility errors
• Create and customize gene filters to adjust fold change and p-value cut-off parameters
• Download publication-ready figures and plots
• Explore pathway, disease, and drug knowledge bases
• Conduct real-time collaboration and results sharing
• Perform multi-omic analyses across experiment and assay types, including ChIP-seq, ATAC-seq, and RNA-seq

Interactive Visualization Features

• Dynamic Volcano and MA plots for differential binding exploration
• Box and bar plots to view protein binding and histone modifications across samples
• Customizable heatmaps with adjustable color palettes
• Motif analysis and peak overlap visualizations
• Genome browser integration
• QC summary dashboards including Q30 scores, alignment rates, duplicate rates, fraction of reads in peaks, genomic regions, and TSS plots
• Peaks-by-region and comparison views

Five-Step ChIP-seq Workflow on ROSALIND

1. Experiment Design: Create a new experiment through a guided setup that captures biological objectives, sample attributes, analysis parameters, NCBI BioProject and BioSample metadata, and custom attributes. ROSALIND supports a broad library of sample and library preparation kits, automatically calibrating each analysis for strandedness, strand direction, unique molecular identifiers (UMIs), and adapters. Antibody selections against proteins and histone marks are also recorded at this stage.
2. ChIP-seq Quality Control: ROSALIND's Quality Control Intelligence automatically evaluates key QC metrics — including Q30 scores (recommended above 85%), alignment rates (recommended above 80%), duplicate rates (recommended below 25%), read trimming rates, sample correlation, and fraction of reads in peaks. Non-aligning reads are evaluated for possible contamination, and researchers can identify and eliminate outlier samples before proceeding to discovery.
3. Unlocking Results: After reviewing quality control, researchers unlock the experiment using Analysis Units (AU), generally calculated at 1 AU per single-sample FASTQ file for ChIP-seq experiments. Account balances and options for acquiring additional AU are accessible directly from the unlock screen.
4. Analysis & Discovery: ROSALIND provides a comprehensive dashboard for differential binding and histone modification interpretation, moving beyond static CSV files. Default filters begin with a fold change of +/- 1.5 and a p-Adjust below 0.05, with further adjustments available. Researchers can create unlimited custom filters, apply gene lists and signatures, explore top pathways, gene ontology, disease associations, and drug interactions through rich interactive plots. New comparisons and meta-analyses — including cross-experiment and multi-omic analyses — can be added at any time and are available within minutes.
5. Collaboration & Data Sharing: ROSALIND Spaces provides virtual data rooms where scientists and collaborators worldwide can 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 a shared environment, with real-time activity feeds and historical reports — all without transferring large files.

ROSALIND is a cloud platform accessible to pharma, biotech, and academic researchers through Enterprise, Professional, and Academic subscriptions, as well as Service Provider, CRO, and Academic Core Lab licenses. The platform accepts both raw FASTQ sequence data and processed counts data, and integrates with NCBI public data models, enabling same-day results and reducing internal bioinformatic workload so scientists can focus directly on the biology of their experiments.