Dahlquist:Protocols

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Lab Organization

• SURP 2015 Schedule
• SURP 2019 Schedule
• 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

Media and Stock Solutions

• YEPD Medium
• YEPD Plates
• Autoclave instructions
• Sodium Phosphate Buffer Recipe

Yeast Cold Shock Project

• 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
• 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

Lactase Persistence Project

• Dahlquist:Evo-Ed Evolution of Lactase Persistence
• Dahlquist:Preparing Cheek Cell Lysate
• Dahlquist:DNA Extraction from Human Hair
• Dahlquist:Lactase Persistence SNP RFLP Analysis
• Dahlquist:TOPO TA Cloning
• Dahlquist:Lactase Persistence Genotyping by qPCR
• Dahlquist:DNA Decontamination
• Claire A. Kosewic Lab Notebook

Real-time PCR (qPCR)

• QPCR_Protocol_Spring2018_Dahlquist.pdf
• Bio-Rad CFX Manager Plate Quick Guide
• PrimerDesign Double-dye Handbook
• 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
• 10 tips for consistent real-time PCR
• Udvardi, M. K., Czechowski, T., & Scheible, W. R. (2008). Eleven golden rules of quantitative RT-PCR. The Plant Cell, 20(7), 1736-1737.
• multiple plates
• How to setup your first qPCR experiment
• Lefever, S., Rihani, A., Van der Meulen, J. et al. Cost-effective and robust genotyping using double-mismatch allele-specific quantitative PCR. Sci Rep 9, 2150 (2019) doi:10.1038/s41598-019-38581-z

Miscellaneous

• Dahlquist:Agarose Gel Electrophoresis
• E. coli Chemically Competent Cell Preparation Protocol
  • Dahlquist:Transformation Protocol for E. coli Chemically Competent Cells
• Kodak Gel Logic 100
• 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
• Dahlquist:DNA Decontamination

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
  • Dahlquist:Clustering Microarray Data with STEM
  • Dahlquist:Between-strain ANOVA
• 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
• Microarray Data Analysis Protocol from the Spring 2017 Biology 478: Molecular Biology of the Genome course
• Microarray Data Analysis Protocol from the Spring 2018 Biology 478: Molecular Biology of the Genome course
• Microarray Data Analysis Protocol from the Spring 2019 Biology 478: Molecular Biology of the Genome course
• Microarray Data Analysis Protocol from the Spring 2020 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
• Dahlquist:Analyzing Yeast Deletion Strain Barcode Sequences
• Dahlquist:BioQUEST Summer Workshop 2018
• Bioinformatics Community Conference 2020 Notes
• Microbiome Resources

COVID-19 Resources

• COVID-19 Research Project page
• BIOL478/S20:SARS-CoV-2 Phylogeny Exercise
• BIOL478/S20:SARS-CoV-2 Spike Protein Structure Exercise
• BIOL478/S20:SARS-CoV-2 Testing Exercise

Literature

Collections

• LitCovid literature database: LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus.
• Coronavirus articles from The Lancet
• Coronavirus: Research, Commentary, and News Collection from Science
  • Coronavirus News from Science

Articles

• Zhou, P., Yang, X., Wang, X. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273 (2020). https://doi.org/10.1038/s41586-020-2012-7
• Xu, Y., Lou, Z., Liu, Y., Pang, H., Tien, P., Gao, G. F., & Rao, Z. (2004). Crystal structure of severe acute respiratory syndrome coronavirus spike protein fusion core. Journal of Biological Chemistry, 279(47), 49414-49419. doi: 10.1074/jbc.M408782200
  • This is the structure from first the first SARS virus.
• Andersen, K.G., Rambaut, A., Lipkin, W.I. et al. The proximal origin of SARS-CoV-2. Nat Med (2020). doi: 10.1038/s41591-020-0820-9
• Hunter, P. (2020) The spread of the COVID‐19 coronavirus. EMBO Rep (2020)e50334, doi: 10.15252/embr.202050334
• Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2. Science. doi: 10.1126/science.abb2762
• Zhang, T., Wu, Q., & Zhang, Z. (2019). Probable Pangolin Origin of 2019-nCoV Associated with Outbreak of COVID-19. CURRENT-BIOLOGY-D-20-00299. doi: 10.1016/j.cub.2020.03.022
• [Moriyama, M., Hugentobler, W. J., & Iwasaki, A. (2020). Seasonality of respiratory viral infections. Annual Review of Virology, 7,1 doi: 10.1146/annurev-virology-012420-022445]
• Liu, Y., Yan, L. M., Wan, L., Xiang, T. X., Le, A., Liu, J. M., ... & Zhang, W. (2020). Viral dynamics in mild and severe cases of COVID-19. The Lancet Infectious Diseases.
• Wan, Y., Shang, J., Graham, R., Baric, R. S., & Li, F. (2020). Receptor recognition by the novel coronavirus from Wuhan: an analysis based on decade-long structural studies of SARS coronavirus. Journal of virology, 94(7).
• Blood vessel attack could trigger coronavirus’ fatal ‘second phase’
• Genetic variant puts African-American populations at greater risk of hydroxychloroquine cardiac complications BioTechniques June 22, 2020
• Teichmann, S., & Regev, A. (2020). The network effect: studying COVID-19 pathology with the Human Cell Atlas. Nature Reviews Molecular Cell Biology, 1-2.

Tracking Number of Cases

• The COVID Tracking Project (USA)
• Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU)
• Worldometers.info
• California Cases Tracked by the LA Times

News & Websites

• Biotechniques: updates to vaccine and therapeutics March 18, 2020
• COVID-19: the medium is the message
• Sigma Xi COVID-19 Preparedness Kit
  • Has a series of links to science articles and other resources for social distancing/online learning
• Jenny Straiton and Caitlin Killen, 16 March 2020, Coronavirus: sorting the fact from the fiction, Biotechniques
• Foldit 1811: Coronavirus Binder Design: Round 3
• Anatomy of a molecule: What makes remdesivir unique? from ASBMB Today, March 17, 2020
• NIH news release about Remdesivir clinical trial
• NIH Coronavirus webpage
• Washington Post: Why Outbreaks like Coronavirus Spread Exponentially and How to Flatten the Curve by Harry Stevens, March 14, 2020
• Gladstone Institutes COVID-19 page
• Food Safety Guide at Serious Eats

Testing

• Protocol for COVID-19 screening using CDC and WHO primers, Version 1.0 (March 14, 2020), by Catie Anderson and Mark Zeller of the Scripps Research Institute
• A serological assay to detect SARS-CoV-2 seroconversion in humans, preprint on MedRxiv
• ClinicalTrials.gov
• Michael J. Loeffelholz & Yi-Wei Tang (2020) Laboratory Diagnosis of Emerging Human Coronavirus Infections — The State of the Art, Emerging Microbes & Infections, DOI: 10.1080/22221751.2020.1745095
• Commercial Test Kit from ThermoFisher(this is not an endorsement)
• Bio-Rad COVID-19 page

Data

• NCBI List of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences
• NCBI Virus
• GISAID: Global Initiative on Sharing All Influenza Data
• Virological.org: A discussion forum for analysis and interpretation of virus molecular evolution and epidemiology.
  • Phylogenetic analysis of nCoV-2019 genomes 6 March 2020
• SARS-CoV-2 sequencing from San Diego county
  • Project page from Andersen lab
• NCBI Genome record for Severe acute respiratory syndrome coronavirus 2, RefSeq ID NC_045512.2
• GenBank record NCBI Reference Sequence: NC_045512.2
• NCBI list of reference genomes
• NCBI list of proteins
• spike protein
• NCBI taxonomy page
• UniProt release notes about SARS-CoV-2
• EMBL-EBI Pathogens page, includes list of PDB records
• PDB Coronavirus page
• COVID-19 Open Research Dataset (CORD-19)

Research Ethics

• Bauchner H, Golub RM, Zylke J. Editorial Concern—Possible Reporting of the Same Patients With COVID-19 in Different Reports. JAMA. Published online March 16, 2020. doi:10.1001/jama.2020.3980
• Jiang, S. (2020) Don’t rush to deploy COVID-19 vaccines and drugs without sufficient safety guarantees Nature 579, 321. doi: 10.1038/d41586-020-00751-9
• COVID-19 retractions put the spotlight on bad data

Teaching Resources

• Crowdsourced teaching resources from the American Society of Microbiology
• Tech & Learning Free Online Learning Resources For Schools Affected by Coronavirus/COVID-19
• Crowdsourced COVID-19 teaching resources
• How Coronavirus Hijacks Your Cells by Jonathan Corum and Carl Zimmer, Updated March 13, 2020
• HHMI Biointeractive can-blood-coronavirus-survivors-treat-newly-ill
• Coronavirus virology video
• 3D Molecular Designs
• COVID-19 resources from ISCB

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)