Research Projects

Skate Genome Project

Skate Genome Project

Background and Objectives

In 2006, the North East IDeA states (VT, NH, ME, RI, DE) launched an initiative now called the North East Cyberinfrastructure Consortium (NECC). Two related collaborative efforts were initiated: to identify and promote the shared use of research facilities across the region, and assess and address cyberinfrastructure needs. This led to the development of the Little Skate Genome Sequencing & Annotation Project, which provides a model for highly collaborative approaches to use specialized resources and expertise in an integrated process.

Collaborative Use of Specialized Resources & Expertise

The project builds on the expertise and resources provided by the Bioinformatics Cores of the five northeastern states that form the NECC, which includes:

  • Little Skate (Leucoraja erinacea) Clones: MDIBL – Mount Desert Island Biological Lab (ME)
  • Next-Generation Sequencing: UD DNA Sequencing & Genotyping Center (DE)
  • Sequence Assembly: Vermont Genetics Network (VT) with ME, RI
  • Sequence Analysis/Annotation: pipeline at DE, ME, RI, NH and VT
  • Storage & Access Of Sequence/Annotation Data: UD shared data center (DE)
  • Public Dissemination: UD CBCB (DE), MDIBL (ME), skatebase.org (VT), NIH

Skate Genome Annotation Workshops

attendees at a bioinformatincs workshop panel discussion

The Skate Genome Annotation Workshops and Jamborees are intended to offer training and opportunities for faculty and students to work with and annotate genome sequences. The workshops include lectures, tutorials and exercises annotating the genome of the little skate, Leucoraja erinacea.

Little Skate Mitochondrial Genome Jamborees
September 2011

Each state held a Mitochondrion Genome Annotation Jamboree bringing together past workshop participants to annotate the complete sequence of the little skate mitochondrial genome sequence. Annotation results from the five states will be combined and reviewed by the organizers. The final annotation and DNA sequence will be submitted to GenBank, and the annotation activities have been summarized and reported in a sumitted manuscript.
http://www.bioinformatics.udel.edu/SkateMitochondrion

Third Skate Genome Annotation Workshop
May 23-27, 2011

This is the final workshop and will be held at the University of Delaware. Topics will include genome annotation basics, overview of automated annotation, GenBank submission tutorial and hands-on annotation exercises.
http://skatebase.org/Workshop_content#ThirdSkateGenomeAnnotation

Second Skate Genome Annotation Workshop
October 12-15, 2010

With nearly two dozen participants, the primary goal of this Skate Genome Annotation Workshop was to train participants in how to annotate skate transcriptome sequences to facilitate annotation of skate genome sequences. This workshop was held at the Mount Desert Island Biological Laboratory.
http://skatebase.org/Workshop_content#SecondSkateGenomeAnnotation

First Skate Genome Annotation Workshop
May 24-28, 2010

The first workshop was held at the University of Delaware and drew 27 student participants and 11 faculty from seven different universities and colleges. Topics included Genome sequencing using Next-Gen, Genome Assembly and Analysis, introduction to sequence, gene and protein resources, sequence similarity searching, genome sequence analysis, gene finding, genome browsers, genome annotation platform and protein bioinformatics.
http://skatebase.org/Workshop_content#FirstSkateGenomeAnnotation

Workshops are sponsored by the IDeA Network for Biomedical Excellence (INBRE) Program from the National Center of Research Resources at the National Institutes of Health (grant number 3P20RR016472-09S2).