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Help & Documentation

Learn how to use the Mini Omics Data Portal tools effectively

Quick Start Guide

Getting Started

  1. 1. Choose a Species: Select your organism of interest from the homepage
  2. 2. Select a Tool: Choose from Genome Browser, Gene Browser, or BLAST Search
  3. 3. Explore Data: Use the interactive tools to analyze your data

Navigation Tips

  • Use the species statistics to understand data scope
  • Tab between tools without losing your work
  • Use "Open in New Tab" for detailed analysis
  • All tools can be opened in new windows for parallel work

Statistics Glossary

The homepage and species pages use the following definitions for portal summary statistics.

Bulk runs

Number of public bulk omics sequencing runs currently included in the portal for this species. Each run usually corresponds to one SRA run accession, such as one SRR record. Multiple runs may be merged into one displayed sample group or genome-browser track.

Bulk bases

Total sequenced bases across the included public bulk runs, based on formal public-source audits plus any documented internal run-level bases evidence when applicable.

SC sample groups

Number of public single-cell sample groups currently included in the portal for this species. Each group corresponds to one public matrix displayed in Dash and can represent one or more source libraries or runs that were merged during curation.

Cells

Total cells across the included public single-cell sample groups, based on the metadata packaged with each published matrix.

Genome Browser

JBrowse 2

Interactive visualization of genomic features, annotations, and sequencing data.

Key Features:
  • Genome navigation
  • Track visualization
  • Feature search
  • Data export
Default Tracks:
  • Ensembl gene models
  • RNA-seq coverage
  • ATAC-seq coverage
  • ChIP-seq coverage
Usage Tips:
  • Use track selector to search by categories, samples, or technologies
  • Click track names to change display settings and colors
  • Search genes by name, ID, or genomic coordinates
  • Use 'Share' button to get links for current view
  • Open in new tab for detailed analysis

Gene Browser

Dash

Interactive gene expression analysis and multi-omics data exploration. Search genes using the sidebar, then explore different data types through the tabs below.

Gene Info

Comprehensive gene annotation and metadata. View basic information including gene ID, name, description, genomic location, and sequence. Explore functional annotations from GO (Gene Ontology) and InterPro domains. For transcription factors, view family classification with links to AnimalTFDB. Find orthologous genes across different species with direct links to their pages.

  • Gene sequences (DNA, CDS, protein)
  • GO terms (BP, MF, CC)
  • InterPro domain annotations
  • Cross-species orthologs
BulkRNA

Visualize bulk RNA-seq expression data across multiple studies and conditions. Select from available studies, each containing multiple samples organized by tissue, developmental stage, or experimental condition. Expression values can be displayed as raw TPM, log-transformed, or z-score normalized for cross-gene comparison.

  • Interactive heatmap visualization
  • Multiple studies selection
  • TPM / Log2 / Z-score transforms
  • Export expression matrix as CSV
scRNA

Explore single-cell RNA-seq data with dimensionality reduction visualizations. View gene expression patterns on UMAP/tSNE embeddings, with cells colored by expression level. Use violin plots to compare expression distributions across cell clusters. Adjust the expression threshold to filter out low-signal noise and highlight cells with significant expression.

  • UMAP/tSNE feature plots
  • Cluster-based violin plots
  • Expression threshold filtering
  • Multiple colorscale options
scATAC

Visualize single-cell chromatin accessibility data. For each gene, view accessibility of associated regulatory peaks on UMAP embeddings. This helps identify cell populations with open chromatin at gene regulatory regions, complementing expression data from scRNA-seq.

  • Peak accessibility on UMAP
  • Gene-associated peak search
  • Accessibility threshold filtering
  • Cluster statistics view
BulkMulti

Integrated multi-omics analysis combining bulk RNA-seq with ATAC-seq data. Explore peak-to-gene linkages that connect regulatory elements to their target genes. View correlation scores between chromatin accessibility and gene expression across samples.

  • Peak-gene linkage visualization
  • Correlation analysis
  • Multi-omics data integration
  • Regulatory region analysis
Landscape

Genomic landscape view showing gene structure, expression profiles, and regulatory connections in genomic context. Visualize how genes relate to nearby regulatory elements and compare expression patterns across the selected genomic region.

  • Genomic region visualization
  • Gene structure display
  • Expression profile tracks
  • Peak-gene linkage arcs
External Links

Gene Browser provides direct links to external databases for additional information:

  • JBrowse: View gene in genomic context with all available tracks
  • Ensembl: Access detailed gene information from Ensembl database
  • AnimalTFDB: Transcription factor family and binding site information
  • InterPro: Protein domain and family classification

BLAST Search

SequenceServer

Find similar sequences in species-specific databases.

Key Features:
  • Multiple BLAST programs
  • Sequence alignment
  • E-value filtering
  • Results download
Available Databases:
  • Genome sequences
  • Ensembl cDNA
  • Reference proteomes
Results Features:
  • Detailed reports and diagrams
  • FASTA sequences download
  • JBrowse links for genome hits
  • Shareable result IDs
Usage Tips:
  • Choose appropriate BLAST program
  • Adjust E-value threshold as needed
  • Use genome database for context
  • Save result IDs for sharing

Data Information

Available Data Types

Genome and Gene Annotations
  • Gene models and features
  • Functional annotations
  • GO and InterPro domains
BLAST Databases
  • Genome sequences
  • cDNA sequences
  • Protein sequences
Bulk Omics Data
  • Bulk RNA-seq
  • Bulk ATAC-seq
  • ChIP-seq
Single-cell Omics Data
  • Single-cell RNA-seq
  • Single-cell ATAC-seq

Available Species

Zebrafish
Zebrafish

Danio rerio

Medaka
Medaka

Oryzias latipes

Turquoise killifish
Turquoise killifish

Nothobranchius furzeri

Mexican Tetra
Mexican Tetra

Astyanax mexicanus

Hydra
Hydra

Hydra vulgaris

Lancelet
Lancelet

Branchiostoma lanceolatum

Cattle
Cattle

Bos taurus

Frequently Asked Questions

Please cite our portal as: "Mini Omics Data Portal. Tu Lab, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. Available at: https://tulab.genetics.ac.cn/miniodp/"

We support standard bioinformatics formats including FASTA, FASTQ, GFF3, GTF, BAM, and various expression matrix formats. Data can be visualized directly in the browser or downloaded for offline analysis.

Data is updated regularly as new datasets become available. Major updates are announced on our homepage. For the most current data version information, please check the individual species pages.

Yes, most data can be downloaded directly from the visualization tools. Gene Browser supports exporting expression matrices as CSV files. Look for download or export options in Genome Browser, Gene Browser, and BLAST Search results pages.

Need Help?

If you have questions about the portal or our datasets, please visit the Tu Lab homepage.

Tu Lab

Institute of Genetics and Developmental Biology

Chinese Academy of Sciences