Deven See Lab

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Lab Forms

• Plate-Layout-Submission-Document-1 (Excel)
• Job Request Form (Word doc)
• Tissue collection and DNA submission instructions (Word doc)
• Genotyping Job Status (Google Sheet)

Due to COVID-19, we are asking that users of the lab sign up with the following links for any equipment they need to use so we can ensure proper social distancing in the lab. Thank you.

• Sign Up remotely for the Zeto/ABI machine(Google Sheet) (How to use ABI sign up sheet (pdf))

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 as its computational capabilities required to handle large data sets generated by the in-house NGS platforms. We have a 32 core, 512GB RAM system for running the various computational jobs in the lab. In addition, there is a 96 core, 1TB RAM high performance computing cluster for massive parallel computation.

Servers

• Supercomputer: WRSGGL01
  32 cores, 512GB RAM total memory
• High Performance Computing Cluster: WRSGGLcluster
  4 compute nodes, 24 cores per node, 256 GB RAM per node, 1TB RAM memory

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]
• [QiAgility]
• 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