Livestock EpiDB: An Integrated Epigenetics and Gene Expression Database & Discovery Resource

Date: Tuesday, January 14, 2014
Time: 1:50 PM
Room: Pacific Salon 6-7 (2nd Floor)
James M. Reecy , Iowa State University, Ames, IA
Eric Fritz-Waters , Department of Animal Science, Iowa State University, Ames, IA
Next-Generation Sequencing (NGS) technologies are allowing researchers to identify whole-genome epigenetic variations at a rapid pace. The cost of generating epigenetic data is dropping, but still considerable at present.  Thus, community resources to process, organize, and share epigenetic data are needed to integrate diverse data types including gene expression data. The objective of the livestock epigenetics database (epiDB) is to provide a community epigenetics repository and bioinformatics resources for the livestock animal community.  Livestock EpiDB consists of four components, including: 1) data capture and achieving; 2) epigenetic and transcript processing; 3) searchable database tools; and 4) data summarization pipelines for data visualization & mining.   Pipelines have been developed to automate the process of data download, processing and database archiving from the NCBI SRA for allele specific expression (ASE), methylation and miRNA information in cattle, chicken, horse and pig. The searchable database was designed to allow users to find features by genomic region, experiment level metadata, species and tissue.  A byproduct of processing the ASE data is the ability to capture transcriptome information from RNAseq experiments.  Reference data tracks will be pre-computed and made available for comparison with future profiling experiments and visualization in a variety of formats (BED, BAM, GFF, VCF).  Future work will facilitate individual user uploads, visualization through epic-CoGe as well as annotation pipelines such as AgBase that facilitate high-throughput data processing at iAnimal.