Dahlquist:Protocols: Difference between revisions
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== Lab Organization == | == Lab Organization == | ||
* [[Dahlquist:SURP 2015 Schedule | SURP 2015 Schedule]] | |||
* [[Media:DahlquistLabSafetyCitizenship.pdf | Laboratory Safety and Citizenship Rules]] | * [[Media:DahlquistLabSafetyCitizenship.pdf | Laboratory Safety and Citizenship Rules]] | ||
* [[Media:Dahlquist_StudentContactInfo.pdf|Student Contact Information Form]] | * [[Media:Dahlquist_StudentContactInfo.pdf|Student Contact Information Form]] | ||
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* [[Media:DahlquistLabCheck-outProcedure.pdf | Check-out Procedure for leaving the lab]] | * [[Media:DahlquistLabCheck-outProcedure.pdf | Check-out Procedure for leaving the lab]] | ||
* [[Media:DahlquistLab_TemperatureLogTemplate.pdf | Temperature Log Template]] (for recording daily temperatures of freezers, incubators, etc.) | * [[Media:DahlquistLab_TemperatureLogTemplate.pdf | Temperature Log Template]] (for recording daily temperatures of freezers, incubators, etc.) | ||
* [[Dahlquist:Letters of Recommendation | How to request letters of recommendation]] | |||
== Wet Lab Protocols == | == Wet Lab Protocols == | ||
* [[Dahlquist:DNA Microarray Protocol | DNA Microarray Protocol]] | * [[Dahlquist:DNA Microarray Protocol | DNA Microarray Protocol]] | ||
* [[Dahlquist:Total RNA Purification from Yeast | Total RNA Purification from Yeast Using the RiboPure Yeast Kit]] | |||
* [[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]] | ||
* [[Dahlquist:RNA-seq Protocol]] | |||
* [[Media:DahlquistLab_YEPDliquidmedia.pdf | YEPD Medium]] | * [[Media:DahlquistLab_YEPDliquidmedia.pdf | YEPD Medium]] | ||
* [[Media:DahlquistLab_YEPDagar.pdf | YEPD Plates]] | * [[Media:DahlquistLab_YEPDagar.pdf | YEPD Plates]] | ||
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** For genotyping yeast systematic deletion strains as adapted for the Dahlquist Lab | ** 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 [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]. | ** 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]. | ||
** [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]] | ||
* [[Media:DahlquistLab_CompetentCellPreparation.doc | E. coli Chemically Competent Cell Preparation Protocol]] | * [[Media:DahlquistLab_CompetentCellPreparation.doc | E. coli Chemically Competent Cell Preparation Protocol]] | ||
** [[Dahlquist:Transformation Protocol for E. coli Chemically Competent Cells]] | ** [[Dahlquist:Transformation Protocol for E. coli Chemically Competent Cells]] | ||
* [[Dahlquist:Kodak Gel Logic 100 | Kodak Gel Logic 100]] | * [[Dahlquist:Kodak Gel Logic 100 | Kodak Gel Logic 100]] | ||
* [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://sageweb.org/files/2-quantifying-yeast-chronological-lifespan-by-outgrowth-of-aged-ce Video on how to use Bioscreen C for yeast aging experiments] | |||
* [https://secure.drierite.com/catalog3/page19b.cfm Regenerating Drierite] | |||
** 1 hour at 210°C/425°F for 1 hour in a single layer on a baking sheet | |||
=== 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 == | ||
* [[Dahlquist:Microarray Data Analysis Workflow]] | |||
** [[Dahlquist:GenePix Pro Software Protocol| GenePix Pro Software Protocol]] | |||
*** [[Media:GenePix.pdf| GenePix Pro Manual 6.0]] | |||
** [[Dahlquist:Microarray Data Processing in R]] | |||
** [[Dahlquist:Modified ANOVA and p value Corrections for Microarray Data]] | |||
* GRNmap | |||
** [[Dahlquist:TRACE Documentation]] | |||
** [[GRNmap_Testing_Report | GRNmap Testing Report Template]] | |||
** [[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. | ||
* [[ | * [[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]] | |||
* [[BIOL478/S15:Microarray Data Analysis | Microarray Data Analysis Protocol from the Spring 2015 Biology 478: Molecular Biology of the Genome course]] | |||
* [[BIOL478/S16:Microarray Data Analysis | Microarray Data Analysis Protocol from the Spring 2016 Biology 478: Molecular Biology of the Genome course]] | |||
* [[BIOL478/S17:Microarray Data Analysis | Microarray Data Analysis Protocol from the Spring 2017 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.) | ||
| Line 43: | Line 68: | ||
* [http://excel2wiki.net/ Converting Excel tables into wiki formatting] | * [http://excel2wiki.net/ Converting Excel tables into wiki formatting] | ||
* [http://library.blackboard.com/ref/e0bedf24-6f8f-48b8-98ec-8ee774e4efde/index.htm Blackboard 9.1 Manual] | * [http://library.blackboard.com/ref/e0bedf24-6f8f-48b8-98ec-8ee774e4efde/index.htm Blackboard 9.1 Manual] | ||
* [[Dahlquist:BioQUEST Summer Workshop 2015]] | |||
** [[Dahlquist:Evo-Ed Evolution of Lactase Persistence]] | |||
* [[Dahlquist:GCAT-SEEK Workshop 2016]] | |||
* [[Dahlquist:GEO Submission 2016]] | |||
* [[Dahlquist:Analyzing Yeast Deletion Strain Barcode Sequences]] | |||
* [[Dahlquist:NIMBioS Working Group May 2017]] | |||
== Reagents == | == Reagents == | ||
Revision as of 14:39, 29 June 2017
Lab Organization
- SURP 2015 Schedule
- 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
- Total RNA Purification from Yeast Using the RiboPure Yeast Kit
- Testing Yeast Strains for Temperature-sensitive Growth on Solid Media
- Dahlquist:RNA-seq Protocol
- 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
- Regenerating Drierite
- 1 hour at 210°C/425°F for 1 hour in a single layer on a baking sheet
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 Analysis Workflow
- GRNmap
- GenMAPP & MAPPFinder Protocols from the Spring 2010 Bioinformatics Lab course.
- 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
- Microarray Data Analysis Protocol from the Spring 2015 Biology 478: Molecular Biology of the Genome course
- Microarray Data Analysis Protocol from the Spring 2016 Biology 478: Molecular Biology of the Genome course
- Microarray Data Analysis Protocol from the Spring 2017 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
- Dahlquist:BioQUEST Summer Workshop 2015
- Dahlquist:GCAT-SEEK Workshop 2016
- Dahlquist:GEO Submission 2016
- Dahlquist:Analyzing Yeast Deletion Strain Barcode Sequences
- Dahlquist:NIMBioS Working Group May 2017
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)
