1. Upload, Display and Analyze Your Data on the Gramene/Ensembl Genome Browser Sushma Naithani (Botany and Plant Pathology, Oregon State University, Corvallis, USA) naithans@science.oregonstate.edu 01/13/2015 PAG 1

2. 2 Pathways 01/13/2015 PAG Gramene Homepage gramene.org

3. 3 Genomes and Genome Browser 01/13/2015 PAG

4. Uploading Data on Genome Browser

5. Users can Add Custom Tracks Salk T-DNA lines Uploaded from my laptop GFF file format EST alignments from non- model plants DAS: Distributed Annotation system Protocol for sharing 3 rd party data DAS Registry Methylome (Ecker) Uploaded from an URL BED file format GFF GTF BED BAM VCF bedGraph Gbrowse PSL WIG BigBed BigWig TrackHub 01/13/2015 PAG

6. Uploading data on Genome Browser 01/13/2015 PAG

7. Variant Effect Predictions 01/13/2015 PAG

8. Configuring Data Display on Genome Browser 01/13/2015 PAG

9. Data Display on Genome Browser 01/13/2015 PAG

10. 10/25/2013 10 SNP and Transcriptome Data Display on Rice Genome Browser 1. SNP data for two rice varieties Pokkali-salinity tolerant and IR29-salinity. 2. Pokkali and IR29 Transcriptomes representing salinity response after 1 hr, 5 hrs and 24 hrs treatments. This data was generated in Pankaj Jaiswal’s lab, OSU.

11. Display of RNA-Seq and SNP Data 01/13/2015 PAG

12. Karyotype view with unique SNPs from Pokkali and IR29 Variant Effect Prediction using SNP data on Rice Genome Browser 01/13/2015 PAG

13. Genome Browser View of Expression Data and SNPs 01/13/2015 PAG Salinity response IR29 Pokkali SNPs

14. Introduction and Overview of Gramene http://www.youtube.com/watch?v=wEaoJTTqWvI Plant Pathways & Gene Expression Analysis http://www.youtube.com/watch?v=umlpHVon1OM Introduction to Plant Reactome http://www.youtube.com/watch?v=wbkuTeIcKjI Webinars and Gramene blog (http://news.gramene.org/) 01/13/2015 PAG

15. 15 01/13/2015 PAG Contact Us!

16. 16 Sign up for Gramene webinar 2015 at Outreach Booth #407 01/13/2015 PAG

17. SAB 2013 Gramene - Exploring Function Through Comparative Genomics and Network Analysis NSF IOS 1127112 Doreen Ware, PI (USDA ARS, CSHL) Kapeel Chougule, Yinping Jiao, Sunita Kumari, Vivek Kumar, Marcela K. Monaco, Andrew Olson, Joshua Stein, Jim Thomason, Peter van Buren, Sharon Wei, Bo Wang, Zhenyuan Lu Pankaj Jaiswal, Co-PI (OSU) Vindhya Amarasinghe, Justin Elser, Sushma Naithani, Justin Preece Paul Kersey & Helen Parkinson (EMBL-EBI) Dan Bolser, Arnaud Kerhornou, Eugene Kulesha, Dan Staines, Brandon Walts / Nuno Fonseca, Maria Keays, Robert Petryszak, Eleanor Williams Lincoln Stein (OICR) Robin Haw; Peter D’Eustachio (NYU); Guanming Wu; David Croft (EBI) Crispin Taylor (ASPB) Patty Lockhart 01/13/2015 PAG