Dahlquist:Protocols

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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
  • Dahlquist:Transformation Protocol for E. coli Chemically Competent Cells
• 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 Analysis Workflow
  • GenePix Pro Software Protocol
    • 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 Template
  • Dahlquist:Sigmoidal Transcriptional Network Model
  • Dahlquist: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
• 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:Evo-Ed Evolution of Lactase Persistence
• Dahlquist:GCAT-SEEK Workshop 2016
• Dahlquist:GEO Submission 2016

Reagents

• List of oligonucleotides/primers in Dahlquist Lab
• Yeast Systematic ORF Deletion Project
  • List of Yeast Deletion Project Primers
• pORF yeast primers FTP site
• HP High-Gloss Photo Paper C6565A (for CS poster plotter)