Quint Lab:Back Door: Difference between revisions
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{{Template:Quint Lab}} | {{Template:Quint Lab}} | ||
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== | ==resources== | ||
*[[primer lists]]<br> | *[[Quint_Lab:primer lists | primer lists]]<br> | ||
*[[enzyme lists]]<br> | *[[Quint_Lab:enzyme lists | enzyme lists]]<br> | ||
*[[seeds]]<br> | *[[Quint_Lab:seeds | seeds]]<br> | ||
*[[ordering | *[[Quint_Lab:ordering | ordering]]<br> | ||
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==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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==online tools== | ==online tools== | ||
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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:// | *[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''''' | ||
*[[ | *[[Quint_Lab:cacl2-competent cells e.coli | cacl2-competent cells e.coli]] | ||
*[[ | *[[Quint_Lab:e.coli transformation chemical | e.coli transformation chemical]] | ||
*[[ | *[[Quint_Lab:electrocompetent cells e.coli | electrocompetent cells e.coli + electroporation]] | ||
*[[ | *[[Quint_Lab:colony pcr | colony pcr]] | ||
*[[ | '''''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]] | ||
*[[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
resources
papers/lab meetings/seminars |
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