Resources
<Clones>
- Aminotransferase genes from E. coli, Arabidopsis, and sorghum were synthesized through the DOE JGI Community Science Program (CSP award 503757) and are available to the scientific community.
- If you are interested in obtaining some of these clones, please look at our DOE project website and contact Hiroshi Maeda, University of Wisconsin-Madison at maeda2@wisc.edu.
<Codes>
- Codes that we used in our studies are made available at Github for Hiroshi Maeda Lab.
Protocols
<Molecular Biology>
- qPCR setup and analysis with the Stratagene Mx3000P
- DNA-free RNA isolation
- Arabidopsis gDNA isolation for Genotyping
- Miniprep, Alkaline Lysis
- qPCR analysis – Agilent Stratagene Mx3000
- RNA isolation from plant tissues
- E. coli competent cell preparation
- Cloning using In-Fusion system (Clontech)
- Site-directed mutagenesis using In-Fusion system
- Sequence analysis
- 1000 Plants (1KP) BLAST
- NCBI Blast
- Fold & Function Assignment System (FFAS)
- Multiple Alignment
- BoxShade
- Select “RTF_new” and “ALN”
- PROMALS3D, structure-guided phylogenetic analysis
- Choose fasta output format in PROMALS3D
- Select all the text and save as a .txt file.
- In MEGA go to File and select “convert file format to mega file”.
- Select the .txt file and specify fasta format. A new window will pop up to save as a new mega file.
- Close out of this
- Go to File, “open file/session”, open the newly created mega file.
- Run phylogenetic analyses.
- Reverse Complement
- Convert Sequence Format
- Translate
- Protein Targeting Prediction (ChloroP, Predotar,TargetP, PSORT)
- SUBA3 (The SUBcellular localisation database for Arabidopsis proteins)
- PhylomeDB (catalogs of gene phylogenies (phylomes)
- Bio.Cyc collection of 7667 Pathway/Genome Databases (PGDBs), plus software tools
- PlaNet visualization and analysis of plant co-function networks
<Biochemistry>
- Protein Modeling using Swiss-Model and PyMOL
<Analytical Chemistry>
<Plant Growth>
Useful links
- Research
- Others