Difference between revisions of "Maeda Lab:Protocols"
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| − | [[Main_Page| <font face=" | + | [[Main_Page| <font face="Georgia" style="color:#ffffff" size=4> '''Home''' </font>]] |
| − | [[Maeda Lab:Research | <font face=" | + | [[Maeda Lab:Research | <font face="Georgia" style="color:#ffffff" size=4> '''Research''' </font>]] |
| − | [[Maeda Lab:Lab | + | [[Maeda Lab:Outreach | <font face="Georgia" style="color:#ffffff" size=4> '''Outreach''' </font>]] |
| − | [[Maeda Lab: | + | [[Maeda Lab:Diversity | <font face="Georgia" style="color:#ffffff" size=4> '''Diversity''' </font>]] |
| − | [[Maeda Lab: | + | [[Maeda Lab:Lab Members | <font face="Georgia" style="color:#ffffff" size=4> '''Team''' </font>]] |
| − | [[Maeda Lab: | + | [[Maeda Lab:Publications | <font face="Georgia" style="color:#ffffff" size=4> '''Pubs''' </font>]] |
| + | [[Maeda Lab:Protocols | <font face="Georgia" style="color:#ffffff" size=5> '''Protocols''' </font>]] | ||
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| + | ==<h3><font>Resources</font></h3>== | ||
| + | '''<Clones>''' | ||
| + | *[https://nfluxmap.github.io/resources/ '''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 [https://nfluxmap.github.io/ '''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 [https://github.com/HiroshiLab Github for '''Hiroshi Maeda Lab''']. | ||
| + | **[https://github.com/HiroshiLab/michaelis-menten R script for evaluating Michaelis-Menten kinetic parameters] | ||
| + | **[https://github.com/HiroshiLab/significance-in-plots ANOVA and Tukey-HSD post-hoc tests] | ||
| + | **[https://github.com/HiroshiLab/Building-gene-trees Building gene trees] | ||
| + | **[https://github.com/HiroshiLab/Evolutionary-rate Evolutionary-rate analysis] | ||
| + | **[https://github.com/HiroshiLab/RNA-seq_data_processing RNAseq data processing] | ||
| + | **[https://github.com/HiroshiLab/GO-term-enrichment GO-term-enrichment] | ||
| + | |||
==<h3><font>Protocols</font></h3>== | ==<h3><font>Protocols</font></h3>== | ||
'''<Molecular Biology>''' | '''<Molecular Biology>''' | ||
| + | *[https://docs.google.com/document/d/1SFVmPU3hrv6QgfDIYMbiLWgTw5jWnHE1lGYT6MST4UE/edit?hl=en_US qPCR setup and analysis with the Stratagene Mx3000P] | ||
| + | *[https://docs.google.com/document/d/17rpTr6tCJyqmCQg79VcNp9c9QXhhYzP11tDUYcCgpZ8/edit?hl=en_US DNA-free RNA isolation] | ||
| + | *[https://docs.google.com/document/d/1vhCZyVIEhJjxj4-6BJNwGO2NvF7ABdfJh3hpNcJOcN4/edit?hl=en_US Arabidopsis gDNA isolation for Genotyping] | ||
| + | *[https://docs.google.com/document/d/1JqZ6lUUrXp6zIKGGdGnp7o3Q7reZvnM9f0HzJX-2Y6A/edit?hl=en_US Miniprep, Alkaline Lysis] | ||
| + | *[https://docs.google.com/document/d/1bS2XFknYLJA4rBGz46rffuToqtD1Iemsyj4jyOMJ7lM/edit?hl=en_US qPCR analysis - Agilent Stratagene Mx3000] | ||
| + | *[https://docs.google.com/document/d/1H9GfxnjfqWXvs36ag3HEFRMSDuNwmosX2WlRz_KtcSs/edit?hl=en_US RNA isolation from plant tissues] | ||
| + | *[https://docs.google.com/document/d/19PbsaLdee5kh71iYKIj8_NW_Pf-ymbTKTuVvtOTqjsk/edit?hl=en_US E. coli competent cell preparation] | ||
| + | *[https://docs.google.com/document/d/1hG9LCIg_SAIKs4ygUTie6RDPOyb-AJ6sX7A6gM0aMvM/edit?hl=en_US Cloning using In-Fusion system (Clontech)] | ||
| + | *[http://www.clontech.com/xxclt_ibcGetAttachment.jsp?cItemId=51246 Site-directed mutagenesis using In-Fusion system] | ||
| + | |||
*Sequence analysis | *Sequence analysis | ||
| + | **[https://www.bioinfodata.org/Blast4OneKP/home 1000 Plants (1KP) BLAST] | ||
**[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast] | **[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast] | ||
| + | **[http://ffas.burnham.org/ffas-cgi/cgi/document.pl Fold & Function Assignment System (FFAS)] | ||
**[http://www.genome.jp/tools/clustalw/ Multiple Alignment] | **[http://www.genome.jp/tools/clustalw/ Multiple Alignment] | ||
**[http://www.ch.embnet.org/software/BOX_form.html BoxShade] | **[http://www.ch.embnet.org/software/BOX_form.html BoxShade] | ||
| + | ***Select "RTF_new" and "ALN" | ||
| + | **[http://prodata.swmed.edu/promals3d/promals3d.php PROMALS3D], structure-guided phylogenetic analysis | ||
| + | ***Choose fasta output format in PROMALS3D | ||
| + | ***Select all the text and save as a .txt file. | ||
| + | ***In [http://www.megasoftware.net 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. | ||
**[http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement] | **[http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement] | ||
**[http://searchlauncher.bcm.tmc.edu/seq-util/Options/readseq.html Convert Sequence Format] | **[http://searchlauncher.bcm.tmc.edu/seq-util/Options/readseq.html Convert Sequence Format] | ||
| + | **[http://web.expasy.org/translate/ Translate] | ||
| + | **Protein Targeting Prediction ([http://www.cbs.dtu.dk/services/ChloroP/ ChloroP], [http://urgi.versailles.inra.fr/predotar/predotar.html Predotar],[http://www.cbs.dtu.dk/services/TargetP/ TargetP], [http://wolfpsort.org/ PSORT]) | ||
| + | **[http://suba.plantenergy.uwa.edu.au/ '''SUBA3'''] (The SUBcellular localisation database for Arabidopsis proteins) | ||
| + | **[http://phylomedb.org/ '''PhylomeDB'''] (catalogs of gene phylogenies (phylomes) | ||
| + | **[http://biocyc.org/ '''Bio.Cyc'''] collection of 7667 Pathway/Genome Databases (PGDBs), plus software tools | ||
| + | **[http://aranet.mpimp-golm.mpg.de/index.html '''PlaNet'''] visualization and analysis of plant co-function networks | ||
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'''<Biochemistry>''' | '''<Biochemistry>''' | ||
| − | * | + | *[https://docs.google.com/document/d/1wmgLCd3zIlKSXvULTslhBf9WeuPCSd1p60aZEGWSEa8/edit?hl=en_US Protein Modeling] using [http://beta.swissmodel.expasy.org/workspace/index.php?func=modelling_beta1 Swiss-Model] and PyMOL |
'''<Analytical Chemistry>''' | '''<Analytical Chemistry>''' | ||
| − | * | + | *[https://docs.google.com/document/d/1SNNU8Tt00PT7ortl0eoq-apoTKpPs2Z3E59xcuNKCdY/edit?hl=en_US Tocopherol analysis - HPLC] |
| + | *[https://docs.google.com/document/d/1hmzLXYnA3e1JUT3Sb6RNIMlpK97tg4WUFixgHLQ0RNQ/edit?hl=en_US Amino acid analysis - HPLC and GCMS] | ||
| + | |||
| + | '''<Plant Growth>''' | ||
| + | *[https://docs.google.com/document/d/1-Q_NTMynHi4ioKyWt2IeykuocoAUPQKYIW0mdoXBm3s/edit?hl=en_US Seed Sterilization - Arabidopsis, Beets] | ||
==<h3><font>Useful links</font></h3>== | ==<h3><font>Useful links</font></h3>== | ||
| − | *[http://chapplewiki.wikispot.org/Protocols Clint Chapple Lab at Purdue University] | + | *Research |
| + | **[http://kanaya.naist.jp/knapsack_jsp/top.html KNApSAcK metabolite-species search] | ||
| + | **[http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE plasmid Editor] | ||
| + | **[http://www.biosci.ohio-state.edu/pcmb/Facilities/abrc/handling.htm Arabidopsis growth ARBC] | ||
| + | **[http://www.phytozome.net/sorghum Sorghum genome blast] | ||
| + | **[http://chapplewiki.wikispot.org/Protocols Clint Chapple Lab at Purdue University] | ||
| + | **[http://www.youtube.com/watch?v=ATh7MljikaA Plasmid Isolation - Mini Prep video] | ||
| + | **[http://medicago-mutant.noble.org/mutant/index.php Noble Foundation Medicago insertional mutant collection] | ||
| + | *Others | ||
| + | **[http://www.ehs.wisc.edu/chem-chemicaldisposalsurplus-chemicalwastesurpluspickuprequestform.htm Waste Pickup Request] | ||
| + | **[http://www.ehs.wisc.edu/chem-chemicaldisposal-surplus.htm UW Madison Chemical Safety Dept (waste disposal etc)] | ||
| + | **[http://kb.wisc.edu/botany/page.php?id=20061 Botany Department IT resources and introduction] | ||
| + | **[http://www.warf.org/inventors/index.jsp?cid=18 Lab Notebook Guidelines from WARF] | ||
| + | **Reference managers: [http://www.mendeley.com/ Mendeley] and [http://www.zotero.org/ Zotero] | ||
| + | **[http://www.library.wisc.edu/delivery/#account-logins How to place an Article and Book request at UW Library] | ||
| + | **[http://www.wikihow.com/Merge-PDF-Files How to merge PDF files] | ||
| − | <h3><font>Media Wiki Editing</font></h3> | + | ==<h3><font>Media Wiki Editing</font></h3>== |
Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. | Consult the [http://meta.wikimedia.org/wiki/Help:Contents User's Guide] for information on using the wiki software. | ||
* [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] | * [http://www.mediawiki.org/wiki/Manual:Configuration_settings Configuration settings list] | ||
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] | * [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ] | ||
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] | * [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list] | ||
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