Quint Lab:Back Door: Difference between revisions

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[[Quint Lab| <font face="trebuchet ms" style="color:#F8B603"> '''home''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
==resources==
[[Quint Lab:Research | <font face="trebuchet ms" style="color:#F8B603"> '''research''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
*[[Quint_Lab:primer lists | primer lists]]<br>
[[Quint Lab:Back Door | <font face="trebuchet ms" style="color:#F8B603"> '''internal''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
*[[Quint_Lab:enzyme lists | enzyme lists]]<br>
[[Quint Lab:Lab Members | <font face="trebuchet ms" style="color:#F8B603"> '''lab members''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
*[[Quint_Lab:seeds | seeds]]<br>
[[Quint Lab:Publications | <font face="trebuchet ms" style="color:#F8B603"> '''publications''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
*[[Quint_Lab:ordering | ordering]]<br>
[[Quint Lab:Teaching | <font face="trebuchet ms" style="color:#F8B603"> '''teaching''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
[[Quint Lab:Contact | <font face="trebuchet ms" style="color:#F8B603"> '''contact''' </font>]] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
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==ressources==
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*[[primer lists]]<br>
*[[enzyme lists]]<br>
*[[seeds]]<br>
*[[ordering]]<br>
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==papers/lab meetings==
*[[papers of the month]]<br>
*[[lab meeting/journal club]]<br>
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==white board==
*awesome video → [http://www.studiodaily.com/main/technique/tprojects/6850.html cellular visions: the inner life of a cell]


==papers/lab meetings/seminars==
*[[Quint_Lab:papers of the month | papers of the month]]<br>
*[[Quint_Lab:lab meeting/journal club | lab meeting/journal club]]
*[http://www.ipb-halle.de/de/allgemeines/veranstaltungen/ ipb progress reports/seminars]
*[http://www.sfb648.uni-halle.de/seminare/ SFB648 seminars]
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==tools==
==online tools==
'''dna/protein analysis:'''
'''dna/protein analysis:'''
*[http://www-bimas.cit.nih.gov/molbio/readseq/ sequence converter]
*[http://www-bimas.cit.nih.gov/molbio/readseq/ sequence converter]
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*[http://www.mcb.harvard.edu/BioLinks/gencode.html genetic code]<br>
*[http://www.mcb.harvard.edu/BioLinks/gencode.html genetic code]<br>
*[http://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj/aastruct.html amino acid structures]<br>
*[http://www.biochem.ucl.ac.uk/bsm/dbbrowser/jj/aastruct.html amino acid structures]<br>
*[http://wishart.biology.ualberta.ca/PlasMapper/ plasmapper]




'''oligos:'''
'''oligos:'''
*[http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/Default.aspx?c=EU oligo analysis]
*[http://eu.idtdna.com/analyzer/Applications/OligoAnalyzer/Default.aspx?c=EU oligo analysis]
*[http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi primer3]
*[http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi primer3plus]
*[http://www.fermentas.com/reviewer/app?page=DuplexAnalysis&service=page duplex analysis]
*[http://www.fermentas.com/reviewer/app?page=DuplexAnalysis&service=page duplex analysis]


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*[http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi blastn]
*[http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi blastn]
*[http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on blastp]
*[http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on blastp]
*[http://nypg.bio.nyu.edu/vicogenta/ Vicogenta - comparing genomes to arabidopsis]




'''arabidopsis tools:'''
'''arabidopsis tools:'''
*[http://www.labutils.de/ rootdetection - automatic measurements of seedling roots and hypocotyls]
*[http://wi.cb.k.u-tokyo.ac.jp/cv/arabimarklet.html arabidopsis database collection]
*[http://www.arabidopsis.org/ tair]
*[http://www.arabidopsis.org/ tair]
*[http://arabidopsis.info/ nasc]
*[http://arabidopsis.info/ nasc]
*[http://www.hort.purdue.edu/hort/facilities/greenhouse/101exp.shtml 101 ways to grow arabidopsis]
*[http://plantsubq.genomics.purdue.edu/ plants-ubq]
*[http://plantsubq.genomics.purdue.edu/ plants-ubq]
*[http://signal.salk.edu/ salk t-dnas]
*[http://signal.salk.edu/ salk t-dnas]
*[https://iii.genevestigator.ethz.ch/at/ genevestigator]
*[https://iii.genevestigator.ethz.ch/at/ genevestigator]
*[http://bbc.botany.utoronto.ca/ efp-browser/expression angler/etc.]
*[http://bbc.botany.utoronto.ca/ efp-browser/expression angler/etc.]
*[http://www.expressionbrowser.com/ GEB - gene expression browser for arabidopsis]
*[http://www.weigelworld.org/resources/microarray/at-tax tiling array expression atlas]
*[http://www.arexdb.org/index.jsp arex]
*[http://www.arexdb.org/index.jsp arex]
*[http://mapman.mpimp-golm.mpg.de/ mapman]
*[http://mapman.mpimp-golm.mpg.de/ mapman]
*[http://wmd.weigelworld.org/cgi-bin/mirnatools.pl web mirna designer]
*[http://wmd.weigelworld.org/cgi-bin/mirnatools.pl web mirna designer]
*[http://jsp.weigelworld.org/tileviz/tileviz.jsp tile viz]
*[http://gbrowse.weigelworld.org/cgi-bin/gbrowse/attax/ tiling array express]
*[http://1001genomes.org/ 1001 genomes]
*[http://polymorph.weigelworld.org/cgi-bin/retrieve_snp.cgi POLYMORPH reseq SNPs]
*[http://ahd.cbi.pku.edu.cn/ arabidopsis hormone database]
*[http://www.jicgenomelab.co.uk/services/genotyping/markers.html JIC microsatellite mapping markers]
*[http://nypg.bio.nyu.edu/vicogenta/ Vicogenta - comparing genomes to arabidopsis]
*[http://amigo.geneontology.org/cgi-bin/amigo/term_enrichment AmiGO - Gene Ontology]
*[http://bioinformatics.psb.ugent.be/plaza/ PLAZA]
*[http://helix.wustl.edu/dcaps/dcaps.html dCAPS finder]
'''medicago tools:'''
*[http://bioinfo.noble.org/gene-atlas/index.php medicago gene expression atlas]
*[http://www.medicago.org/ medicago database]




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*[http://polymorph.weigelworld.org/cgi-bin/retrieve_snp.cgi polymorph - reseq. snps]
*[http://polymorph.weigelworld.org/cgi-bin/retrieve_snp.cgi polymorph - reseq. snps]
*[http://www.atprimer.tsl.ac.uk/cgi-bin/form1.cgi atprimer ecotypes]
*[http://www.atprimer.tsl.ac.uk/cgi-bin/form1.cgi atprimer ecotypes]
 
*[http://www.jicgenomelab.co.uk/services/genotyping/markers.html JIC microsatellite mapping markers]
*[http://bbc.botany.utoronto.ca/markertracker/index.spy Marker Tracker]
*[http://bergelson.uchicago.edu/a.thaliana-resources Bergelson A.thaliana Resources]
*[http://www.onekp.com/ The 1kp project - 1000 plant genomes]


'''calculators:'''
'''calculators:'''
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*[http://www.fermentas.com/reviewer/app?page=Calculator&service=external&sp=Sconcentrations concentration conversions - molar units ↔ weight/volume]
*[http://www.fermentas.com/reviewer/app?page=Calculator&service=external&sp=Sconcentrations concentration conversions - molar units ↔ weight/volume]
*[http://www.sigmaaldrich.com/Life_Science/Molecular_Biology/PCR/Key_Resources/PCR_Tools.html pcr mastermix calculator]
*[http://www.sigmaaldrich.com/Life_Science/Molecular_Biology/PCR/Key_Resources/PCR_Tools.html pcr mastermix calculator]
*[http://www.sigmaaldrich.com/Area_of_Interest/Research_Essentials/Biological_Buffers/Key_Resources/BufferCalc/SigmaAldrich_Buffer_Calculator.html buffer calculator]
*[http://www.sigmaaldrich.com/Life_Science/Molecular_Biology/PCR/Key_Resources/PCR_Tools.html pcr mastermix calculator]
*[[Media:Stammloesung.swf|Konzrechner]]
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==white board==
*[http://www.johnkyrk.com/evolution.html evolution time line animated]
*[https://www.youtube.com/watch?v=xJG0ir9nDtc lab safety rap]
*[http://192.124.243.170/wordpress AG Quint - Lab Blog]
*[http://www.metablast.org/downloads - Meta!Blast real-time 3D action-adventure game to explore the vivid, dynamic world of a soybean plant cell - might be worth a try!]
*[http://dfg-science-tv.de/ DFG Science TV]: Forscher stellen ihre eigenen Projekte vor
*[http://www.thirteen.org/naturally-obsessed/ Naturally Obsessed: The making of a Scientist - documentary]
*[http://trailblazing.royalsociety.org/? historical papers of the royal society]
*[http://professorsciencemusic.googlepages.com/home professor science]
*[http://bitesizebio.com/2007/09/10/free-pc-software-for-molecular-biologists/ free PC software for molecular biologists]
*[http://bitesizebio.com/2009/06/22/six-important-factors-for-successful-reverse-transcription/ Six Important Factors for Reverse Transcription]
*[http://www.youtube.com/watch?v=Er4MsAVs9hQ Video: Jede Zelle ...]
*[http://www.spiegel.de/video/video-57928.html Video: GFP-tagged HIV infiziert T-Zelle]
*[http://www.youtube.com/watch?v=f6aU-wFSqt0&eurl=http://www.spiegel.de/wissenschaft/mensch/0,1518,575773,00.html The Large Hadron Rap]
*[http://bioinfo.noble.org/gene-atlas/index.php medicago gene expression atlas]
*[http://www.nature.com/naturejobs/2008/080515/full/nj7193-424b.html the postdoc interview]
*craig venter's grand vision on synthetic genomics → [http://www.ted.com/talks/view/id/227 video]
*Kits and their unique role in molecular biology: [http://www.biotechniques.com/default.asp?page=supplements&subsection=article_display&display=full&id=112796&year=2008&issue=4/1/2008  a brief retrospective]
*[http://bitesizebio.com/2008/04/30/re-cycling-electroporation-cuvettes/ recycling electroporation cuvettes]
*[http://bitesizebio.com/2008/04/28/pimp-your-plasmid-growth-medium/  pimp your plasmid growth medium]
*[http://www.sigmaaldrich.com/Area_of_Interest/Research_Essentials/Biological_Buffers/Key_Resources/BufferCalc/SigmaAldrich_Buffer_Calculator.html buffer calculator]
*[http://bitesizebio.com/2008/04/14/lab-remote-desktop/ Control Your Lab Computers From Home]
*run faster gels → [http://bitesizebio.com/2008/04/09/faster-gels/ new electrophoresis buffers]
*how-to-become-a-world-expert-in-your-field → [http://bitesizebio.com/2008/03/31/how-to-become-a-world-expert-in-your-field/ artikel]
*[http://bitesizebio.com/2008/04/02/quick-and-dirty-screening-for-cloned-inserts/ quick and dirty] screening for cloned inserts
*awesome video → [http://www.studiodaily.com/main/technique/tprojects/6850.html cellular visions: the inner life of a cell]
*[http://www.jove.com Journal of Visualized Experiments]
 
 
 
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==lab protocols==  
==lab protocols==  
→ check also [http://www.openwetware.org/wiki/Protocols openwetware protocols]
→ check also [http://www.openwetware.org/wiki/Protocols openwetware protocols]<br>
*[[arabidopsis dna isolation - quick and dirty]]
 
*[[arabidopsis transformation]]
'''''e. coli'''''
*[[ems mutagenesis]]
*[[Quint_Lab:cacl2-competent cells e.coli | cacl2-competent cells e.coli]]
*[[colony pcr]]
*[[Quint_Lab:e.coli transformation chemical | e.coli transformation chemical]]
*[[cacl2-competent cells e.coli]]
*[[Quint_Lab:electrocompetent cells e.coli | electrocompetent cells e.coli + electroporation]]
*[[electrocompetent cells e.coli]]
*[[Quint_Lab:colony pcr | colony pcr]]
*[[agrobacterium plasmid miniprep]]
'''''agros'''''
*[[ats plates]]
*[[Quint_Lab:preparing electrocompetent A.rhizogenes cells + electroporation | electrocompetent A.rhizogenes cells + electroporation ]]
*[[iaa extraction and quantification]]
*[[Quint_Lab:agrobacterium plasmid miniprep | agrobacterium plasmid miniprep]]
*[[ligation (sticky ends)]]
 
*[[northern]]
'''''arabidopsis'''''
*[[western]]
*[[Media:southern.pdf | southern blot]]
*[[e.coli transformation chemical]]
*[[Quint_Lab:arabidopsis dna isolation - quick and dirty | arabidopsis dna isolation - quick and dirty]]
*[[Quint_Lab:arabidopsis transformation | arabidopsis transformation]]
*[[Quint_Lab:arabidopsis protoplast transformation | arabidopsis protoplast transformation]]
*[[Quint_Lab:arabidopsis rna isolation protocols (including siliques) | arabidopsis rna isolation protocols (including siliques)]]
*[[Quint_Lab:transient transformation and expression| transient transformation and expression]]
*[[Quint_Lab:kanamycin selection of transgenic seeds | kanamycin selection of transgenic seeds]]
*[[Media:basta.pdf |  selection of transgenic seeds on basta plates ]]
*[[Quint_Lab:ems mutagenesis | ems mutagenesis]]
*[[Quint_Lab:ats plates | ats plates]]
*[[Quint_Lab:iaa extraction and quantification | iaa extraction and quantification]]
 
'''yeast'''<br>
→ for general yeast handling follow Clontech [http://www.clontech.com/images/pt/PT3024-1.pdf Yeast Protocols Handbook] <br>
→ for Y2H follow Clontech [http://www.clontech.com/images/pt/PT3955-1.pdf Matchmaker Library Construction & Screening Kit]
*[[Quint_Lab:yeast dna isolation | genomic dna]]
*[[Quint_Lab:non-lethal ß-galactosidase assay | non-lethal ß-galactosidase assay]]
*[[Quint_Lab:Short version ß-galactosidase assay | Short version ß-galactosidase assay]]
*[[Quint_Lab:yeast plasmid prep | plasmid prep]]
*[[Quint_Lab:yeast transformation  | yeast transformation ]]
*[[Quint_Lab:yeast western blot  | yeast western blot ]]
*[[Quint_Lab:yeast mating in 24-well plates  | mating in 24-well plates ]]
*[[Quint_Lab:yeast media  | yeast media ]]
 
 
'''general'''
*[[Quint_Lab:ligation (sticky ends) | ligation (sticky ends)]]
*[[Quint_Lab:northern | northern]]
*[[Quint_Lab:western | western]]
 
 
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Revision as of 01:32, 4 March 2013

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<wikionly>|width=395px style="padding: 5px; background-color: #ffffff; border: 2px solid #000101;" |

resources

papers/lab meetings/seminars

</wikionly>

online tools

dna/protein analysis:


oligos:


blasts/alignments:


arabidopsis tools:


medicago tools:


natural variation/polymorphisms:

calculators:

white board


lab protocols

→ check also openwetware protocols

e. coli

agros

arabidopsis

yeast
→ for general yeast handling follow Clontech Yeast Protocols Handbook
→ for Y2H follow Clontech Matchmaker Library Construction & Screening Kit


general


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