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Updated: Jun 5, 2025
07:27
Transcriptome Analysis of Single Cells
Published on: April 25, 2011
29.8K
Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome
Muskan Kapoor1, Enrique Sapena Ventura2, Amy Walsh3
1Department of Animal Science, Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States.
Frontiers in Genetics
|December 16, 2024
Summary
This study integrates livestock single-cell RNA sequencing data into the Terra platform using FAANG standards. This enables advanced analysis and visualization, promoting FAIR data principles in agricultural genomics.
Area of Science:
- Agricultural Genomics
- Bioinformatics
- Single-cell Genomics
Background:
- Existing agricultural genomics data submission standards are underdeveloped for single-cell (SC) data.
- Human genomics infrastructure (Human Cell Atlas Data Portal, Terra) and EMBL-EBI's Single Cell Expression Atlas offer advanced capabilities.
- The FAANG data portal lacks computational links to these resources, hindering agricultural genomics research.
Purpose of the Study:
- To assess the feasibility of using FAANG metadata standards for ingesting livestock scRNA-seq data into Terra.
- To develop and extend data tools for seamless integration and analysis of agricultural SC data.
- To establish a FAIR data resource for agricultural species genomics.
Main Methods:
- Leveraged Human Cell Atlas Data Portal and Terra platform.
- Utilized EMBL-EBI's Single Cell Expression Atlas for data ingestion.
- Adapted FAANG metadata standards for scRNA-seq data.
- Developed semi-automated metadata brokering and data transfer workflows.
- Verified data ingestion into Terra and performed scRNA-seq analysis on porcine data.
- Created prototype visualization tools using JBrowse.
Main Results:
- Demonstrated successful ingestion of scRNA-seq datasets into Terra using FAANG standards.
- Implemented semi-automated metadata brokering for scRNA-seq data, reducing expert curation needs.
- Validated data transfer from HCA Data Portal to Terra for analysis.
- Executed a workflow for analyzing the first ingested porcine scRNA-seq dataset.
- Developed JBrowse visualization tracks for comparing scRNA-seq and bulk RNA-seq data.
Conclusions:
- FAANG metadata standards can be adapted for ingesting livestock scRNA-seq data into Terra.
- Developed tools facilitate data sharing, analysis, and visualization for agricultural genomics.
- The project lays the foundation for a FAIR data ecosystem for agricultural species genomics.
