Dahlquist:Protocols: Difference between revisions
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* [[Dahlquist:SURP 2015 Schedule | SURP 2015 Schedule]] | * [[Dahlquist:SURP 2015 Schedule | SURP 2015 Schedule]] | ||
* [[ | * [[Dahlquist:SURP 2019 Schedule | SURP 2019 Schedule]] | ||
* [[Media:Dahlquist_StudentContactInfo.pdf|Student Contact Information Form]] | * [[Media:Dahlquist_StudentContactInfo.pdf|Student Contact Information Form]] | ||
* [[Media:DahlquistLabNotebookGuidelines.pdf | Guidelines for Paper Laboratory Notebooks]] | * [[Media:DahlquistLabNotebookGuidelines.pdf | Guidelines for Paper Laboratory Notebooks]] | ||
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== Wet Lab Protocols == | == Wet Lab Protocols == | ||
=== Media and Stock Solutions === | |||
* [[Media:DahlquistLab_YEPDliquidmedia.pdf | YEPD Medium]] | * [[Media:DahlquistLab_YEPDliquidmedia.pdf | YEPD Medium]] | ||
* [[Media:DahlquistLab_YEPDagar.pdf | YEPD Plates]] | * [[Media:DahlquistLab_YEPDagar.pdf | YEPD Plates]] | ||
* [[Media:DahlquistLab_AutoclaveInstructions.pdf | Autoclave instructions]] | * [[Media:DahlquistLab_AutoclaveInstructions.pdf | Autoclave instructions]] | ||
* [https://www.msu.edu/~eisthen/lab/methods/anatomy/recipes/PB.html Sodium Phosphate Buffer Recipe] | |||
=== Yeast Cold Shock Project === | |||
* [[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]] | |||
* [[Dahlquist:RNA-seq Protocol]] | |||
* [[Media:DahlquistLab_ColonyPCRProtocol_YeastDeletionStrains.doc | Yeast Colony PCR]] | * [[Media:DahlquistLab_ColonyPCRProtocol_YeastDeletionStrains.doc | Yeast Colony PCR]] | ||
** For genotyping yeast systematic deletion strains as adapted for the Dahlquist Lab | ** For genotyping yeast systematic deletion strains as adapted for the Dahlquist Lab | ||
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** [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.] | ** [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]] | ||
=== Real-time PCR === | === 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) === | |||
* [[Media: QPCR_Protocol_Spring2018_Dahlquist.pdf | QPCR_Protocol_Spring2018_Dahlquist.pdf]] | |||
* [http://www.bio-rad.com//webroot/web/pdf/lsr/literature/PN_10010421.pdf Bio-Rad CFX Manager Plate Quick Guide] | * [http://www.bio-rad.com//webroot/web/pdf/lsr/literature/PN_10010421.pdf Bio-Rad CFX Manager Plate Quick Guide] | ||
* [http://www.primerdesign.co.uk/assets/files/double_dye_handbook.pdf?timestamp=1516139856 PrimerDesign Double-dye Handbook] | |||
* [http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_039283.pdf ABI TaqMan Gene Expression Master Mix Quick Reference Card] | * [http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_039283.pdf ABI TaqMan Gene Expression Master Mix Quick Reference Card] | ||
* [http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_039284.pdf ABI TaqMan Gene Expression Master Mix Protocol] | * [http://www3.appliedbiosystems.com/cms/groups/mcb_support/documents/generaldocuments/cms_039284.pdf ABI TaqMan Gene Expression Master Mix Protocol] | ||
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* [http://medgen.ugent.be/~jvdesomp/genorm/ geNorm software] | * [http://medgen.ugent.be/~jvdesomp/genorm/ geNorm software] | ||
* [http://www.expertqpcr.com/ expertqpcr software] | * [http://www.expertqpcr.com/ expertqpcr software] | ||
* [https://bitesizebio.com/1118/10-tips-for-consistent-real-time-pcr-rtpcr/ 10 tips for consistent real-time PCR] | |||
* [https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2518243/ Udvardi, M. K., Czechowski, T., & Scheible, W. R. (2008). Eleven golden rules of quantitative RT-PCR. The Plant Cell, 20(7), 1736-1737.] | |||
* [https://www.slideshare.net/idtdna/high-throughput-qpcr-tips-for-analysis-across-multiple-plates multiple plates] | |||
* [http://gregdijkman.com/setup-first-qPCR-experiment How to setup your first qPCR experiment] | |||
* [https://www.nature.com/articles/s41598-019-38581-z 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]] | |||
* [[Media:DahlquistLab_CompetentCellPreparation.doc | E. coli Chemically Competent Cell Preparation Protocol]] | |||
** [[Dahlquist:Transformation Protocol for E. coli Chemically Competent Cells]] | |||
* [[Dahlquist:Kodak Gel Logic 100 | Kodak Gel Logic 100]] | |||
* [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 | |||
* [[Dahlquist:DNA Decontamination]] | |||
== Dry Lab Protocols == | == Dry Lab Protocols == | ||
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** [[Dahlquist:Microarray Data Processing in R]] | ** [[Dahlquist:Microarray Data Processing in R]] | ||
** [[Dahlquist:Modified ANOVA and p value Corrections for Microarray Data]] | ** [[Dahlquist:Modified ANOVA and p value Corrections for Microarray Data]] | ||
** [[Dahlquist:Clustering Microarray Data with STEM]] | |||
** [[Dahlquist:Between-strain ANOVA]] | |||
* GRNmap | * GRNmap | ||
** [[Dahlquist:TRACE Documentation]] | |||
** [[GRNmap_Testing_Report | GRNmap Testing Report Template]] | ** [[GRNmap_Testing_Report | GRNmap Testing Report Template]] | ||
** [[Dahlquist:Sigmoidal Transcriptional Network Model]] | ** [[Dahlquist:Sigmoidal Transcriptional Network Model]] | ||
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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]] | |||
* [[BIOL478/S18:Microarray_Data_Analysis | Microarray Data Analysis Protocol from the Spring 2018 Biology 478: Molecular Biology of the Genome course]] | |||
* [[BIOL478/S19:Microarray_Data_Analysis | Microarray Data Analysis Protocol from the Spring 2019 Biology 478: Molecular Biology of the Genome course]] | |||
* [[BIOL478/S20:Microarray_Data_Analysis | Microarray Data Analysis Protocol from the Spring 2020 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:BioQUEST Summer Workshop 2018]] | |||
* [[Dahlquist:BCC 2020 | Bioinformatics Community Conference 2020 Notes]] | |||
* [[Dahlquist:Microbiome Resources | Microbiome Resources]] | |||
=== COVID-19 Resources === | |||
* [[Dahlquist:COVID-19 Research Project | 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 ===== | |||
* [https://www.ncbi.nlm.nih.gov/research/coronavirus/ LitCovid literature database]: LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. | |||
* [https://www.thelancet.com/coronavirus?dgcid=kr_pop-up_tlcoronavirus20 Coronavirus articles from ''The Lancet''] | |||
* [https://www.sciencemag.org/coronavirus-research-commentary-and-news?intcmp=ghd_cov Coronavirus: Research, Commentary, and News Collection from ''Science''] | |||
** [https://www.sciencemag.org/tags/coronavirus Coronavirus News from ''Science''] | |||
===== Articles ===== | |||
* [https://doi.org/10.1038/s41586-020-2012-7 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] | |||
* [https://www.jbc.org/content/279/47/49414.full 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). [https://rdcu.be/b24wo doi: 10.1038/s41591-020-0820-9] | |||
* Hunter, P. (2020) The spread of the COVID‐19 coronavirus. EMBO Rep (2020)e50334, [https://doi.org/10.15252/embr.202050334 doi: 10.15252/embr.202050334] | |||
* [https://science.sciencemag.org/content/early/2020/03/03/science.abb2762.abstract 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] | |||
* [https://www.cell.com/current-biology/fulltext/S0960-9822(20)30360-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0960982220303602%3Fshowall%3Dtrue 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] | |||
* [https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30232-2/fulltext 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.] | |||
* [https://jvi.asm.org/content/94/7/e00127-20 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).] | |||
* [https://www.sciencemag.org/news/2020/06/blood-vessel-attack-could-trigger-coronavirus-fatal-second-phase?utm_campaign=ScienceNow&utm_medium=Facebook&utm_source=JHubbard Blood vessel attack could trigger coronavirus’ fatal ‘second phase’] | |||
* [https://www.biotechniques.com/coronavirus-news/genetic-variant-puts-african-american-populations-at-greater-risk-of-hydroxychloroquine-cardiac-complications/ ''Genetic variant puts African-American populations at greater risk of hydroxychloroquine cardiac complications'' BioTechniques June 22, 2020] | |||
* [https://www.nature.com/articles/s41580-020-0267-3 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 ==== | |||
* [https://covidtracking.com/data/ The COVID Tracking Project (USA)] | |||
* [https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6 Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU)] | |||
* [https://www.worldometers.info/coronavirus/ Worldometers.info] | |||
* [https://www.latimes.com/projects/california-coronavirus-cases-tracking-outbreak/ California Cases Tracked by the LA Times] | |||
==== News & Websites ==== | |||
* [https://www.biotechniques.com/coronavirus-news/coronavirus-updates-to-vaccine-and-therapeutic-development/?utm_source=Adestra&utm_medium=email&utm_term=&utm_content=Coronavirus%3A%20updates%20to%20vaccine%20and%20therapeutic%20development&utm_campaign=Daily%20NL%202020-03-23 Biotechniques: updates to vaccine and therapeutics March 18, 2020] | |||
* [https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30600-0/fulltext COVID-19: the medium is the message] | |||
* [https://www.sigmaxi.org/programs/critical-issues-in-science/covid-19-preparedness-kit Sigma Xi COVID-19 Preparedness Kit] | |||
** Has a series of links to science articles and other resources for social distancing/online learning | |||
* [https://www.biotechniques.com/coronavirus-news/coronavirus-sorting-the-fact-from-the-fiction/?utm_source=Adestra&utm_medium=email&utm_term=&utm_content=Coronavirus%3A%20sorting%20the%20fact%20from%20the%20fiction&utm_campaign=Daily%20NL%202020-03-19 Jenny Straiton and Caitlin Killen, 16 March 2020, Coronavirus: sorting the fact from the fiction, ''Biotechniques''] | |||
* [https://fold.it/portal/node/2009030 Foldit 1811: Coronavirus Binder Design: Round 3] | |||
* [https://www.asbmb.org/asbmb-today/science/031720/what-makes-remdesivir-a-promising-antiviral?utm_source=emailer Anatomy of a molecule: What makes remdesivir unique? from ASBMB Today, March 17, 2020] | |||
* [https://www.nih.gov/news-events/news-releases/nih-clinical-trial-remdesivir-treat-covid-19-begins NIH news release about Remdesivir clinical trial] | |||
* [https://www.nih.gov/health-information/coronavirus NIH Coronavirus webpage] | |||
* [https://www.washingtonpost.com/graphics/2020/world/corona-simulator/ Washington Post: Why Outbreaks like Coronavirus Spread Exponentially and How to Flatten the Curve by Harry Stevens, March 14, 2020] | |||
* [https://gladstone.org/COVID-19?utm_source=Cell+Signals+-+External+Email+List&utm_campaign=6614bed873-EMAIL_CAMPAIGN_COVID-19-update&utm_medium=email&utm_term=0_f25fc65fc1-6614bed873-119764585 Gladstone Institutes COVID-19 page] | |||
* [https://www.seriouseats.com/2020/03/food-safety-and-coronavirus-a-comprehensive-guide.html Food Safety Guide at Serious Eats] | |||
==== Testing ==== | |||
* [https://docs.google.com/document/d/1fi3Sd7BIpQGe1VZyEqxzlAbzSOUplhlrOyvpAx-iXE0/edit 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 | |||
* [https://www.medrxiv.org/content/10.1101/2020.03.17.20037713v1 A serological assay to detect SARS-CoV-2 seroconversion in humans, preprint on MedRxiv] | |||
* [https://clinicaltrials.gov/ct2/results?cond=%22wuhan+coronavirus%22 ClinicalTrials.gov] | |||
* [https://www.tandfonline.com/doi/full/10.1080/22221751.2020.1745095 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] | |||
* [https://www.thermofisher.com/us/en/home/clinical/clinical-genomics/pathogen-detection-solutions/coronavirus-2019-ncov/genetic-analysis/taqpath-rt-pcr-covid-19-kit.html?icid=WB44096 Commercial Test Kit from ThermoFisher](this is not an endorsement) | |||
* [https://www.bio-rad.com/featured/en/coronavirus-covid-19-assay-development-vaccine-research.html?WT.mc_id=200324027902&mkt_tok=eyJpIjoiWkdFMU5UazRPV1l4WW1KaiIsInQiOiJXZm9Sa3RzbFdmVVlsMEZFNXBzVzh4MW44U0tZelwvSit5T3NFaGxHNm5GaG9OaXYxeEQ3Q1J3SzlvblVWU004azhQdEdtWmZ0SEhqbXFVbE96Q2J4TGEwM1J2eU9TdzZWaVR0WnFSc2UrTTgxS1wvMml2TnNNdzBDZW82RmVqRFowIn0%3D Bio-Rad COVID-19 page] | |||
==== Data ==== | |||
* [https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/ NCBI List of SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) Sequences] | |||
* [https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&SeqType_s=Nucleotide NCBI Virus] | |||
* [https://www.gisaid.org/ GISAID: Global Initiative on Sharing All Influenza Data] | |||
* [http://virological.org/ Virological.org: A discussion forum for analysis and interpretation of virus molecular evolution and epidemiology.] | |||
** [http://virological.org/t/phylodynamic-analysis-176-genomes-6-mar-2020/356 Phylogenetic analysis of nCoV-2019 genomes 6 March 2020] | |||
* [https://www.ncbi.nlm.nih.gov/bioproject/612578 SARS-CoV-2 sequencing from San Diego county] | |||
** [https://andersen-lab.com/secrets/data/hcov-19-genomics/ Project page from Andersen lab] | |||
* [https://www.ncbi.nlm.nih.gov/genome/?term=txid2697049 NCBI Genome record for Severe acute respiratory syndrome coronavirus 2, RefSeq ID NC_045512.2] | |||
* [https://www.ncbi.nlm.nih.gov/nuccore/1798174254 GenBank record NCBI Reference Sequence: NC_045512.2] | |||
* [https://www.ncbi.nlm.nih.gov/genome/genomes/86693 NCBI list of reference genomes] | |||
* [https://www.ncbi.nlm.nih.gov/genome/proteins/86693?genome_assembly_id=757732 NCBI list of proteins] | |||
* [https://www.ncbi.nlm.nih.gov/gene/43740568 spike protein] | |||
* [https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2697049 NCBI taxonomy page] | |||
* [https://www.uniprot.org/news/2020/02/26/release UniProt release notes about SARS-CoV-2] | |||
* [https://www.ebi.ac.uk/ena/pathogens/covid-19 EMBL-EBI Pathogens page], includes list of PDB records | |||
* [http://www.rcsb.org/news?year=2020&article=5e3c4bcba5007a04a313edcc PDB Coronavirus page] | |||
* [https://pages.semanticscholar.org/coronavirus-research COVID-19 Open Research Dataset (CORD-19)] | |||
==== Research Ethics ==== | |||
* [https://jamanetwork.com/journals/jama/fullarticle/2763371 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] | |||
* [https://www.nature.com/articles/d41586-020-00751-9 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] | |||
* [https://www.biotechniques.com/coronavirus-news/opinion_covid-19-retractions-put-the-spotlight-on-bad-data/?utm_campaign=BioTechniques&utm_medium=email&_hsmi=89261972&_hsenc=p2ANqtz-8kHSUeArgvCMwqYFKaQd4w2RN-upDG0QE7gHrrD3gf23SGGo1N9LSfFrYDHrGRkMpgbulEM3oJDZ59j3eou7FKsWZA7Q&utm_content=89261972&utm_source=hs_email COVID-19 retractions put the spotlight on bad data] | |||
==== Teaching Resources ==== | |||
* [https://docs.google.com/spreadsheets/d/17m1gUVprX8CqYP5P0ijnkLBtD-zkPdgvkKnjQyiSE8k/edit#gid=0 Crowdsourced teaching resources from the American Society of Microbiology] | |||
* [https://www.techlearning.com/resources/free-online-learning-resources-for-schools-affected-by-coronaviruscovid-19 Tech & Learning Free Online Learning Resources For Schools Affected by Coronavirus/COVID-19] | |||
* [https://docs.google.com/document/d/1GEqswVZDie5aVgM_Fbs5lFeWPdpAOL-2HqS59vb-21o/edit Crowdsourced COVID-19 teaching resources] | |||
* [https://www.nytimes.com/interactive/2020/03/11/science/how-coronavirus-hijacks-your-cells.html How Coronavirus Hijacks Your Cells by Jonathan Corum and Carl Zimmer, Updated March 13, 2020] | |||
* [https://www.biointeractive.org/planning-tools/science-news/can-blood-coronavirus-survivors-treat-newly-ill HHMI Biointeractive can-blood-coronavirus-survivors-treat-newly-ill] | |||
* [https://www.youtube.com/watch?v=8_bOhZd6ieM Coronavirus virology video] | |||
* [https://www.3dmoleculardesigns.com/The-Science-of-Coronaviruses.htm 3D Molecular Designs] | |||
* [https://www.iscb.org/covid19 COVID-19 resources from ISCB] | |||
== Reagents == | == Reagents == |
Latest revision as of 12:39, 16 January 2024
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)