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.
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)
Graduate Students
Staff
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
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
Undergraduates
Ajanna Dizon
Major: Biochemistry
Anaï Holguín-Yanez
Major:
Esmeralda Valverde
Major:
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