Dahlquist:Protocols: Difference between revisions
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* [https://www.msu.edu/~eisthen/lab/methods/anatomy/recipes/PB.html Sodium Phosphate Buffer Recipe] | * [https://www.msu.edu/~eisthen/lab/methods/anatomy/recipes/PB.html Sodium Phosphate Buffer Recipe] | ||
* [http://www.ambion.com/techlib/misc/oligo_calculator.html Oligo Extinction Coefficient Calculator] | * [http://www.ambion.com/techlib/misc/oligo_calculator.html Oligo Extinction Coefficient Calculator] | ||
* [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] | |||
=== Real-time PCR === | === Real-time PCR === | ||
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* [http://www.mdl.dk/publicationsnormfinder.htm NormFinder software] | * [http://www.mdl.dk/publicationsnormfinder.htm NormFinder software] | ||
* [http://medgen.ugent.be/~jvdesomp/genorm/ geNorm software] | * [http://medgen.ugent.be/~jvdesomp/genorm/ geNorm software] | ||
* [http://www.expertqpcr.com/ expertqpcr software] | |||
== Dry Lab Protocols == | == Dry Lab Protocols == | ||
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* [[Dahlquist:Microarray Data Processing in R]] | * [[Dahlquist:Microarray Data Processing in R]] | ||
* [[Dahlquist:Modified ANOVA and p value Corrections for Microarray Data]] | * [[Dahlquist:Modified ANOVA and p value Corrections for Microarray Data]] | ||
* [[Dahlquist:Sigmoidal Transcriptional Network Model]] | |||
* [[Dahlquist:GRNmap]] | |||
* [[BIOL398-01/S10:GenMAPP_and_MAPPFinder_Protocols | GenMAPP & MAPPFinder Protocols]] from the Spring 2010 Bioinformatics Lab course. | * [[BIOL398-01/S10:GenMAPP_and_MAPPFinder_Protocols | GenMAPP & MAPPFinder Protocols]] from the Spring 2010 Bioinformatics Lab course. | ||
* [[Dahlquist:GenePix Pro Software Protocol| GenePix Pro Software Protocol]] | * [[Dahlquist:GenePix Pro Software Protocol| GenePix Pro Software Protocol]] | ||
* [[Media:GenePix.pdf| GenePix Pro Manual 6.0]] | * [[Media:GenePix.pdf| GenePix Pro Manual 6.0]] | ||
* [[BIOL478/S13:Microarray_Data_Analysis | Microarray Data Analysis Protocol from the Spring 2013 Biology 478: Molecular Biology of the Genome course]] | |||
* [[BIOL478/S14:Microarray_Data_Analysis | Microarray Data Analysis Protocol from the Spring 2014 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.) | ||
Revision as of 13:43, 21 July 2014
Lab Organization
- Laboratory Safety and Citizenship Rules
- Student Contact Information Form
- Guidelines for Paper Laboratory Notebooks
- Check-out Procedure for leaving the lab
- Temperature Log Template (for recording daily temperatures of freezers, incubators, etc.)
- How to request letters of recommendation
Wet Lab Protocols
- DNA Microarray Protocol
- Testing Yeast Strains for Temperature-sensitive Growth on Solid Media
- YEPD Medium
- YEPD Plates
- Autoclave instructions
- Yeast Colony PCR
- For genotyping yeast systematic deletion strains as adapted for the Dahlquist Lab
- To download the file of primer sequences and product sizes, right click on 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 SGD.
- 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.
- Scanning instructions GenePix 4000B
- E. coli Chemically Competent Cell Preparation Protocol
- Kodak Gel Logic 100
- Sodium Phosphate Buffer Recipe
- Oligo Extinction Coefficient Calculator
- Video on how to use Bioscreen C for yeast aging experiments
Real-time PCR
- Bio-Rad CFX Manager Plate Quick Guide
- ABI TaqMan Gene Expression Master Mix Quick Reference Card
- ABI TaqMan Gene Expression Master Mix Protocol
- ABI Guide to Performing Relative Quantitation of Gene Expression Using Real-Time Quantitative PCR
- 10 Tips for consistent real-time PCR
- NormFinder software
- geNorm software
- expertqpcr software
Dry Lab Protocols
- Dahlquist:Microarray Data Processing in R
- Dahlquist:Modified ANOVA and p value Corrections for Microarray Data
- Dahlquist:Sigmoidal Transcriptional Network Model
- Dahlquist:GRNmap
- GenMAPP & MAPPFinder Protocols from the Spring 2010 Bioinformatics Lab course.
- GenePix Pro Software Protocol
- GenePix Pro Manual 6.0
- Microarray Data Analysis Protocol from the Spring 2013 Biology 478: Molecular Biology of the Genome course
- Microarray Data Analysis Protocol from the Spring 2014 Biology 478: Molecular Biology of the Genome course
- Edge Software Protocol
- Edge Manual (Note: I posted this because I could no longer find a link to it on the web.)
- Dahlquist:Wiki Checklist
- Changing Drive Letters on Windows XP and 7
- Converting Excel tables into wiki formatting
- Blackboard 9.1 Manual
Reagents
- List of oligonucleotides/primers in Dahlquist Lab
- Yeast Systematic ORF Deletion Project
- pORF yeast primers FTP site
- HP High-Gloss Photo Paper C6565A (for CS poster plotter)
