Dahlquist:Protocols

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* [[Media:Dahlquist_StudentContactInfo.pdf‎|Student Contact Information Form]]
* [[Media:Dahlquist_StudentContactInfo.pdf‎|Student Contact Information Form]]
* [[Media:DahlquistLabNotebookGuidelines.pdf | Guidelines for Paper Laboratory Notebooks]]
* [[Media:DahlquistLabNotebookGuidelines.pdf | Guidelines for Paper Laboratory Notebooks]]
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* [[Media:DahlquistLabCheck-outProcedure.pdf | Check-out Procedure for leaving the lab]]
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* [[Media:DahlquistLab_TemperatureLogTemplate.pdf | Temperature Log Template]] (for recording daily temperatures of freezers, incubators, etc.)
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* [[Dahlquist:Letters of Recommendation | How to request letters of recommendation]]
== Wet Lab Protocols ==
== Wet Lab Protocols ==
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* [[Dahlquist:DNA Microarray Protocol | DNA Microarray Protocol]]: this protocol is under construction.
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* [[Dahlquist:DNA Microarray Protocol | DNA Microarray Protocol]]
* [[Media:DahlquistLab_Temperature-sensitiveGrowthProtocol.doc | Testing Yeast Strains for Temperature-sensitive Growth on Solid Media]]
* [[Media:DahlquistLab_Temperature-sensitiveGrowthProtocol.doc | Testing Yeast Strains for Temperature-sensitive Growth on Solid Media]]
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* YEPD Medium
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* [[Media:DahlquistLab_YEPDliquidmedia.pdf | YEPD Medium]]
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* YEPD Plates
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* [[Media:DahlquistLab_YEPDagar.pdf | YEPD Plates]]
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* Yeast Colony PCR
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* [[Media:DahlquistLab_AutoclaveInstructions.pdf | Autoclave instructions]]
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* Bacterial Colony PCR
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* [[Media:DahlquistLab_ColonyPCRProtocol_YeastDeletionStrains.doc | Yeast Colony PCR]]
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** For genotyping yeast systematic deletion strains as adapted for the Dahlquist Lab
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** To download the file of primer sequences and product sizes, right click on [http://www-sequence.stanford.edu/group/yeast_deletion_project/Deletion_primers_PCR_sizes.txt this link] and choose "Save target as" or "Save link as".  The file is a tab-delimited text file that then can be opened in Excel.  The file uses the systematic name (ORF ID) for the genes which can be looked up at [http://yeastgenome.org SGD].
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** [http://www.biotechniques.com/multimedia/archive/00160/BTN5005-BM-Kristjuh_160476a.pdf Protocol for quick purification of genomic DNA from yeast for PCR (Looke et al. 2011, ''Biotechniques'' 50(5): 325–328); haven't tried this yet, just bookmarking it here.]
* [[Media:ScannerInstructions.doc | Scanning instructions GenePix 4000B]]
* [[Media:ScannerInstructions.doc | Scanning instructions GenePix 4000B]]
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* [[Media:DahlquistLab_CompetentCellPreparation.doc | E. coli Chemically Competent Cell Preparation Protocol]]
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** [[Dahlquist:Transformation Protocol for E. coli Chemically Competent Cells]]
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* [[Dahlquist:Kodak Gel Logic 100 | Kodak Gel Logic 100]]
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* [https://www.msu.edu/~eisthen/lab/methods/anatomy/recipes/PB.html Sodium Phosphate Buffer Recipe]
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* [http://www.ambion.com/techlib/misc/oligo_calculator.html Oligo Extinction Coefficient Calculator]
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* [http://sageweb.org/files/2-quantifying-yeast-chronological-lifespan-by-outgrowth-of-aged-ce Video on how to use Bioscreen C for yeast aging experiments]
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=== Real-time PCR ===
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* [http://www.bio-rad.com//webroot/web/pdf/lsr/literature/PN_10010421.pdf Bio-Rad CFX Manager Plate Quick Guide]
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* [http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_039283.pdf ABI TaqMan Gene Expression Master Mix Quick Reference Card]
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* [http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_039284.pdf ABI TaqMan Gene Expression Master Mix Protocol]
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* [http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_042380.pdf ABI Guide to Performing Relative Quantitation of Gene Expression Using Real-Time Quantitative PCR]
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* [http://bitesizebio.com/2009/01/20/10-tips-for-consistent-real-time-pcr-rtpcr/ 10 Tips for consistent real-time PCR]
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* [http://www.mdl.dk/publicationsnormfinder.htm NormFinder software]
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* [http://medgen.ugent.be/~jvdesomp/genorm/ geNorm software]
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* [http://www.expertqpcr.com/ expertqpcr software]
== Dry Lab Protocols ==
== Dry Lab Protocols ==
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* [[Dahlquist:Microarray Data Processing in R]]
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* [[Dahlquist:Modified ANOVA and p value Corrections for Microarray Data]]
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* [[Dahlquist:Sigmoidal Transcriptional Network Model]]
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* [[Dahlquist:Michaelis-Menten Transcriptional Network Model]]
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* [[BIOL398-01/S10:GenMAPP_and_MAPPFinder_Protocols | GenMAPP & MAPPFinder Protocols]] from the Spring 2010 Bioinformatics Lab course.
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* [[Dahlquist:GenePix Pro Software Protocol| GenePix Pro Software Protocol]]
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* [[Media:GenePix.pdf| GenePix Pro Manual 6.0]]
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* [[BIOL478/S13:Microarray_Data_Analysis | Microarray Data Analysis Protocol from the Spring 2013 Biology 478: Molecular Biology of the Genome course]].
* [[Dahlquist:Edge Software Protocol | Edge Software Protocol]]
* [[Dahlquist:Edge Software Protocol | Edge Software Protocol]]
* [[Media:Edge_manual.pdf | Edge Manual]] (Note:  I posted this because I could no longer find a link to it on the web.)
* [[Media:Edge_manual.pdf | Edge Manual]] (Note:  I posted this because I could no longer find a link to it on the web.)
* [[Dahlquist:Wiki Checklist]]
* [[Dahlquist:Wiki Checklist]]
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* [[Dahlquist:General Computer Management | Changing Drive Letters on Windows XP]]
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* [[Dahlquist:General Computer Management | Changing Drive Letters on Windows XP and 7]]
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* [http://excel2wiki.net/ Converting Excel tables into wiki formatting]
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* [http://library.blackboard.com/ref/e0bedf24-6f8f-48b8-98ec-8ee774e4efde/index.htm Blackboard 9.1 Manual]
== Reagents ==
== Reagents ==
* [[Media:DahlquistLab_Primers.xls | List of oligonucleotides/primers in Dahlquist Lab]]
* [[Media:DahlquistLab_Primers.xls | List of oligonucleotides/primers in Dahlquist Lab]]
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* Yeast Systematic Deletion Project
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* [http://www-sequence.stanford.edu/group/yeast_deletion_project/protocols.html Yeast Systematic ORF Deletion Project]
** [http://www-sequence.stanford.edu/group/yeast_deletion_project/Deletion_primers_PCR_sizes.txt List of Yeast Deletion Project Primers]
** [http://www-sequence.stanford.edu/group/yeast_deletion_project/Deletion_primers_PCR_sizes.txt List of Yeast Deletion Project Primers]
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* [http://downloads.yeastgenome.org/sequence/primer_sequences/ pORF yeast primers FTP site]
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* HP High-Gloss Photo Paper C6565A (for CS poster plotter)

Revision as of 13:49, 10 May 2013

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Contents

Lab Organization

Wet Lab Protocols

Real-time PCR

Dry Lab Protocols

Reagents

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