Deven See Lab

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Lab Forms

• Plate Layout Submission Document (Excel)
• Job Request Form (Word doc)
• Tissue collection and DNA submission instructions (Word doc)

Data

• 42K SNP Consensus map with Physical Position (Excel)
• Known Informative Markers (GMS) (Excel)
• List of Varieties with Available Exome Capture and Promoter Capture Data (Excel)

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Graduate Students

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Staff

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Computational Capacity

The See Lab contracts with the USDA to use the SCINet High-performance Computing Systems. We have access to 48 core, 350 GB memory nodes for standards jobs, as well as a high-mem 1.5 TB node. In addition, there is also a 128 core, 1TB dedicated GPU node for massively-parallel jobs.

Storage

• Supercomputer
• HPC
• Independent RAID storage

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Technologies, Equipment & Capabilities

Next-Gen Sequencing

• Illumina NextSeq®500
  • 400 million reads/12hours
  • Exome Sequencing
  • Targeted Gene Sequencing (amplicon, gene panel)
  • Whole-Transcriptome Sequencing
  • Cytogenomic Arrays

Sanger Sequencing

• ABI 3730

Fragment Analysis

• SSR
• STS
• CAP

DNA Extraction

• Bead Shaker
• Oktopure
• Synergy Microplate Reader (Quantification)
• QiAgility

SNP Analysis

• KASP
• Synergy Microplate Reader
• Genotype by Multiplex Sequencing (GMS)
• Exome Capture

Software

• GeneMarker (v1.5,v1.9) [Soft Genetics]
• Gen5 2.0 [BioTek/Synergy Plate reader]
• JMP Genomics
• Multipoint
• MultiQTL
• TASSEL

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Undergraduates

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Former Members

• Dolores Covarrubias, Research Technician
• Amandeep Dhaliwal, Research Technician
• Esraa Alwan, Ph.D. Crop and Soil Sciences
• Kanokporn Triwitayakorn, Fulbright Visiting Scientist
• Taras Nazarov, Ph.D. Plant Pathology
• Jennifer Logan, Research Technician
• Jinita Sthapit, Ph.D. Plant Pathology
• Vandhana Krishnan, Associate in Research, Bioinformatician
• Derick Jiwan, Post-Doctoral Researcher, Crop Sciences
• Jonathan Eagle, M.S. Plant Pathology
• Sajal Sthapit, Ph.D. Plant Pathology
• Yan Liu, Ph.D. Plant Pathology
• Marcus Hooker, Ph.D. Plant Pathology