Dahlquist:Protocols: Difference between revisions
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* [[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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* [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] | * [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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** [[Dahlquist:Modified ANOVA and p value Corrections for Microarray Data]] | ** [[Dahlquist:Modified ANOVA and p value Corrections for Microarray Data]] | ||
* GRNmap | * GRNmap | ||
** [[Dahlquist: GRNmap Testing Report Template]] | ** [[Dahlquist:TRACE Documentation]] | ||
** [[GRNmap_Testing_Report | GRNmap Testing Report Template]] | |||
** [[Dahlquist:Sigmoidal Transcriptional Network Model]] | ** [[Dahlquist:Sigmoidal Transcriptional Network Model]] | ||
** [[Dahlquist:GRNmap]] | ** [[Dahlquist:GRNmap]] | ||
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* [[BIOL478/S14:Microarray_Data_Analysis | Microarray Data Analysis Protocol from the Spring 2014 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/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.) | ||
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* [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)
