Maeda Lab:Protocols

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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. R script for evaluating Michaelis-Menten kinetic parameters ANOVA and Tukey-HSD post-hoc tests Building gene trees Evolutionary-rate analysis RNAseq data processing GO-term-enrichment 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> Tocopherol analysis - HPLC Amino acid analysis - HPLC and GCMS <Plant Growth> Seed Sterilization - Arabidopsis, Beets Useful links Research KNApSAcK metabolite-species search ApE plasmid Editor Arabidopsis growth ARBC Sorghum genome blast Clint Chapple Lab at Purdue University Plasmid Isolation - Mini Prep video Noble Foundation Medicago insertional mutant collection Others Waste Pickup Request UW Madison Chemical Safety Dept (waste disposal etc) Botany Department IT resources and introduction Lab Notebook Guidelines from WARF Reference managers: Mendeley and Zotero How to place an Article and Book request at UW Library How to merge PDF files Media Wiki Editing Consult the User's Guide for information on using the wiki software. Configuration settings list MediaWiki FAQ MediaWiki release mailing list Wikitable code Header 1 Header 2 Header 3 row 1 cell 1 row 1 cell 2 row 1 cell 3 row 2 cell 1 row 2 cell 2 row 2 cell 3