Dahlquist:Protocols
From OpenWetWare
Jump to navigationJump to search
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
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
- 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
- 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: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
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.
- SARS-CoV-2 sequencing from San Diego county
- 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
- pORF yeast primers FTP site
- HP High-Gloss Photo Paper C6565A (for CS poster plotter)
