Difference between revisions of "Maeda Lab:Protocols"

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<h3><font>Protocols</font></h3>
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==<h3><font>Resources</font></h3>==
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*'''Molecular Biology'''
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'''<Clones>'''
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**Sequence analysis
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*[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.
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***[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
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**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.
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***[http://www.genome.jp/tools/clustalw/ Multiple Alignment]
 
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***[http://www.ch.embnet.org/software/BOX_form.html BoxShade]
 
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***[http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement]
 
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***[http://searchlauncher.bcm.tmc.edu/seq-util/Options/readseq.html Convert Sequence Format]
 
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***
 
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**qPCR primer design [https://www.roche-applied-science.com/sis/rtpcr/upl/index.jsp?id=UP030000 (Roche ProbeFinder Version: 2.45)]
 
  
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<h3><font>Useful links</font></h3>
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'''<Codes>'''
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*[http://chapplewiki.wikispot.org/Protocols Clint Chapple Lab at Purdue University]
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*Codes that we used in our studies are made available at [https://github.com/HiroshiLab Github for '''Hiroshi Maeda Lab'''].
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**[https://github.com/HiroshiLab/michaelis-menten R script for evaluating Michaelis-Menten kinetic parameters]
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**[https://github.com/HiroshiLab/significance-in-plots ANOVA and Tukey-HSD post-hoc tests]
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**[https://github.com/HiroshiLab/Building-gene-trees Building gene trees]
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**[https://github.com/HiroshiLab/Evolutionary-rate Evolutionary-rate analysis]
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**[https://github.com/HiroshiLab/RNA-seq_data_processing RNAseq data processing]
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**[https://github.com/HiroshiLab/GO-term-enrichment GO-term-enrichment]
  
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<h3><font>Media Wiki Editing</font></h3>
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==<h3><font>Protocols</font></h3>==
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'''<Molecular Biology>'''
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*[https://docs.google.com/document/d/1SFVmPU3hrv6QgfDIYMbiLWgTw5jWnHE1lGYT6MST4UE/edit?hl=en_US qPCR setup and analysis with the Stratagene Mx3000P]
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*[https://docs.google.com/document/d/17rpTr6tCJyqmCQg79VcNp9c9QXhhYzP11tDUYcCgpZ8/edit?hl=en_US DNA-free RNA isolation]
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*[https://docs.google.com/document/d/1vhCZyVIEhJjxj4-6BJNwGO2NvF7ABdfJh3hpNcJOcN4/edit?hl=en_US Arabidopsis gDNA isolation for Genotyping]
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*[https://docs.google.com/document/d/1JqZ6lUUrXp6zIKGGdGnp7o3Q7reZvnM9f0HzJX-2Y6A/edit?hl=en_US Miniprep, Alkaline Lysis]
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*[https://docs.google.com/document/d/1bS2XFknYLJA4rBGz46rffuToqtD1Iemsyj4jyOMJ7lM/edit?hl=en_US qPCR analysis - Agilent Stratagene Mx3000]
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*[https://docs.google.com/document/d/1H9GfxnjfqWXvs36ag3HEFRMSDuNwmosX2WlRz_KtcSs/edit?hl=en_US RNA isolation from plant tissues]
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*[https://docs.google.com/document/d/19PbsaLdee5kh71iYKIj8_NW_Pf-ymbTKTuVvtOTqjsk/edit?hl=en_US E. coli competent cell preparation]
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*[https://docs.google.com/document/d/1hG9LCIg_SAIKs4ygUTie6RDPOyb-AJ6sX7A6gM0aMvM/edit?hl=en_US Cloning using In-Fusion system (Clontech)]
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*[http://www.clontech.com/xxclt_ibcGetAttachment.jsp?cItemId=51246 Site-directed mutagenesis using In-Fusion system]
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 +
*Sequence analysis
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**[https://www.bioinfodata.org/Blast4OneKP/home 1000 Plants (1KP) BLAST]
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**[http://blast.ncbi.nlm.nih.gov/Blast.cgi NCBI Blast]
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**[http://ffas.burnham.org/ffas-cgi/cgi/document.pl Fold & Function Assignment System (FFAS)]
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**[http://www.genome.jp/tools/clustalw/ Multiple Alignment]
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**[http://www.ch.embnet.org/software/BOX_form.html BoxShade]
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***Select "RTF_new" and "ALN"
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**[http://prodata.swmed.edu/promals3d/promals3d.php PROMALS3D], structure-guided phylogenetic analysis
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***Choose fasta output format in PROMALS3D
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***Select all the text and save as a .txt file.
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***In [http://www.megasoftware.net MEGA] go to File and select "convert file format to mega file".
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***Select the .txt file and specify fasta format. A new window will pop up to save as a new mega file.
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***Close out of this
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***Go to File, "open file/session", open the newly created mega file.
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***Run phylogenetic analyses.
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**[http://www.bioinformatics.org/sms/rev_comp.html Reverse Complement]
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**[http://searchlauncher.bcm.tmc.edu/seq-util/Options/readseq.html Convert Sequence Format]
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**[http://web.expasy.org/translate/ Translate]
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**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])
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**[http://suba.plantenergy.uwa.edu.au/ '''SUBA3'''] (The SUBcellular localisation database for Arabidopsis proteins)
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**[http://phylomedb.org/ '''PhylomeDB'''] (catalogs of gene phylogenies (phylomes)
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**[http://biocyc.org/ '''Bio.Cyc'''] collection of 7667 Pathway/Genome Databases (PGDBs), plus software tools
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**[http://aranet.mpimp-golm.mpg.de/index.html '''PlaNet'''] visualization and analysis of plant co-function networks
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 +
'''<Biochemistry>'''
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*[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
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'''<Analytical Chemistry>'''
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*[https://docs.google.com/document/d/1SNNU8Tt00PT7ortl0eoq-apoTKpPs2Z3E59xcuNKCdY/edit?hl=en_US Tocopherol analysis - HPLC]
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*[https://docs.google.com/document/d/1hmzLXYnA3e1JUT3Sb6RNIMlpK97tg4WUFixgHLQ0RNQ/edit?hl=en_US Amino acid analysis - HPLC and GCMS]
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 +
'''<Plant Growth>'''
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*[https://docs.google.com/document/d/1-Q_NTMynHi4ioKyWt2IeykuocoAUPQKYIW0mdoXBm3s/edit?hl=en_US Seed Sterilization - Arabidopsis, Beets]
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 +
==<h3><font>Useful links</font></h3>==
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*Research
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**[http://kanaya.naist.jp/knapsack_jsp/top.html KNApSAcK metabolite-species search]
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**[http://biologylabs.utah.edu/jorgensen/wayned/ape/ ApE plasmid Editor]
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**[http://www.biosci.ohio-state.edu/pcmb/Facilities/abrc/handling.htm Arabidopsis growth ARBC]
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**[http://www.phytozome.net/sorghum Sorghum genome blast]
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**[http://chapplewiki.wikispot.org/Protocols Clint Chapple Lab at Purdue University]
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**[http://www.youtube.com/watch?v=ATh7MljikaA Plasmid Isolation - Mini Prep video]
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**[http://medicago-mutant.noble.org/mutant/index.php Noble Foundation Medicago insertional mutant collection]
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*Others
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**[http://www.ehs.wisc.edu/chem-chemicaldisposalsurplus-chemicalwastesurpluspickuprequestform.htm Waste Pickup Request]
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**[http://www.ehs.wisc.edu/chem-chemicaldisposal-surplus.htm UW Madison Chemical Safety Dept (waste disposal etc)]
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**[http://kb.wisc.edu/botany/page.php?id=20061 Botany Department IT resources and introduction]
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**[http://www.warf.org/inventors/index.jsp?cid=18 Lab Notebook Guidelines from WARF]
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**Reference managers: [http://www.mendeley.com/ Mendeley] and [http://www.zotero.org/ Zotero]
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**[http://www.library.wisc.edu/delivery/#account-logins How to place an Article and Book request at UW Library]
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**[http://www.wikihow.com/Merge-PDF-Files How to merge PDF files]
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==<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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Latest revision as of 15:15, 15 March 2023

Maeda lab banner 2020.jpg

Home        Research        Outreach        Diversity        Team        Pubs        Protocols       


Resources

<Clones>

<Codes>

Protocols

<Molecular Biology>


<Biochemistry>

<Analytical Chemistry>

<Plant Growth>

Useful links

Media Wiki Editing

Consult the User's Guide for information on using the wiki software.

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