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Associated Publications |
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CRISPR-Enhance Lateral Flow Assay Resource Report Resource Website |
Piyush Jain, Long T Nguyen, Santosh Rananaware | 10.17504/protocols.io.bk5zky76 | Jain Lab | The CRISPR-Enhance SARS-CoV-2 detection kit has been designed to detect fragments of the Nucleocapsid (“N”) gene and Envelope gene (E) of SARS-CoV-2. An included third target is the human RNase P POP7 gene (“RP”) which serves as a control for the extraction of the clinical sample in the absence of a positive SARS-CoV-2 result.The entire reaction from RT-LAMP amplification to CRISPR-based detection of the target analytes can be performed in approximately one hour.The CRISPR-Enhance kit comprises of two steps. Step one is a reverse transcriptase loop-mediated amplification (RT-LAMP) where targeted SARS-CoV-2 genomic RNA is reverse transcribed to DNA, and this DNA is amplified by a strand-displacing DNA polymerase. Step two is the transcription of the amplified DNA to activate the collateral cleavage activity of a CRISPR complex programmed to the target RNA sequence. This collateral activity results in cleavage of nucleic acid reporters, resulting in a visual readout using a paper strip in appoximately 2 mins. | University of Florida, University of Florida, University of Florida | 1 | 2020 | Piyush Jain, Long T Nguyen, Santosh Rananaware 2020. CRISPR-Enhance Lateral Flow Assay. protocols.io dx.doi.org/10.17504/protocols.io.bk5zky76 | 2021-03-29 03:10:32 | |||
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Supplemental Resources for You Can’t Hide Your Lying Eyes: Honesty Oaths and Misrepresentation Resource Report Resource Website |
J Jobu Babin, Haritima Chauhan, Feng Liu | 10.17504/protocols.io.bix3kfqn | AbstractLying about personal qualifications for a job or in college admissions is common and has recently become a high profile issue. In this paper, we explore the decision to misrepresent one’s self and subsequently determine whether honesty oaths impact truthful reporting of a personal characteristic. To do this, we execute a field experiment on Amazon MTurk using a self-reporting task involving worker eye color. We provide empirical evidence that honesty oaths elicit more truthful behavior, primarily impacting “extreme” lies. Oath-taking decreased the cost associated with misreporting personal characteristics by 70%. Oaths marginally decrease shirking. | Western Illinois University, Western Illinois University, Western Illinois University | 2 | 2020 | J Jobu Babin, Haritima Chauhan, Feng Liu 2020. Supplemental Resources for You Can’t Hide Your Lying Eyes: Honesty Oaths and Misrepresentation. protocols.io dx.doi.org/10.17504/protocols.io.bix3kfqn | 2021-03-29 03:10:33 | ||||
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Creating Tensor Maps Resource Report Resource Website |
Courtney Comrie | 10.17504/protocols.io.8jyhupw | This protocol will provide a basic guide creating Tensor maps.Note: Steps may vary based upon data. | University of Arizona | 1 | 2020 | Courtney Comrie 2020. Creating Tensor Maps. protocols.io dx.doi.org/10.17504/protocols.io.8jyhupw | 2021-03-29 03:10:33 | ||||
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Basic Protocol 2: Tagging a gene of interest with AID Resource Report Resource Website |
Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin | 10.17504/protocols.io.bdyei7te | The next step in developing the ARF-AID system is to tag the gene of interest with AID. The ARF-AID system requires full-length AID (Figure 1) because the characterized interaction domains of AID with ARF are domains III and IV. Domains I and II are involved in the interaction with TIR1. The mini-AID lacks domains III and IV and will not interact with ARF to stabilize the protein in the absence of auxin (Sathyan et al., 2019). Note that the antibiotic selection marker (HygroR) is co-transcribed with AID and the protein products are separated during translation. Therefore, the resistance marker will be expressed at levels comparable to the target protein. | Biochemistry and Molecular Genetics Department, University of Virginia, Biochemistry and Molecular Genetics Department, University of Virginia, Biochemistry and Molecular Genetics Department, University of Virginia ; Center for Public Health Genomics, University of Virginia; Cancer Center, University of Virginia | 1 | 2020 | Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin 2020. Basic Protocol 2: Tagging a gene of interest with AID. protocols.io dx.doi.org/10.17504/protocols.io.bdyei7te | 2021-03-29 03:10:32 | ||||
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NEBExpress MBP Fusion and Purification System (NEB #E8201) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.bfayjifw | New England Biolabs (NEB) | The NEBExpress MBP Fusion and Purification System takes advantage of the strong Ptac promoter and the translation initiation signals of maltose binding protein (MBP) to enhance solubility and expression levels of a desired protein inE. coli. The resulting product is an MBP fusion protein, which is then purified by affinity chromatography.ReliableE. coli expression: substantial yields (up to 100 mg/L)Fusion to MBP has been shown to enhance the solubility of proteins expressed inE. coli(1)Two-step purification: amylose elution followed by TEV Protease cleavage and Ni resin isolation results in a highly pure tag-free target proteinGentle elution with maltose; no detergents or harsh denaturants required | New England Biolabs | https://www.neb.com/protocols/2020/02/05/nebexpress-mbp-fusion-and-purification-system-quick-start-protocol-neb-e8201 | 1 | 2020 | New England Biolabs 2020. NEBExpress MBP Fusion and Purification System (NEB #E8201). protocols.io dx.doi.org/10.17504/protocols.io.bfayjifw | 2021-03-29 03:10:32 | ||
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16S Universal Bacterial PCR Resource Report Resource Website |
Matthew Sullivan | 10.17504/protocols.io.dfr3m5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab | 1 | 2016 | Matthew Sullivan 2016. 16S Universal Bacterial PCR. protocols.io dx.doi.org/10.17504/protocols.io.dfr3m5 | 2021-03-29 03:10:29 | ||||
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Protocol for washing and modifying QCM-D sensors Resource Report Resource Website |
Victoria Linderberg | 10.17504/protocols.io.ex6bfre | Thomas Crouzier Lab | This protocol describes how to wash QCM-D sensors before usage and how to modify their surface using a composition of symmetric (poly)ethylene glycol (PEG) thiols consisting of 99% dS-PEG and 1% dS-PEG-biotin. | 2 | 2016 | Victoria Linderberg 2016. Protocol for washing and modifying QCM-D sensors. protocols.io dx.doi.org/10.17504/protocols.io.ex6bfre | 2021-03-29 03:10:29 | ||||
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Script P3: Open Reading Frame Prediction Resource Report Resource Website |
HANNIGAN GC, GRICE EA, ET AL | 10.17504/protocols.io.efpbbmn | VERVE Net, Club Grice | This protocol provides a method for predicting the locations of the open reading frames (ORFs) using the Glimmer3 toolkit. Methods based on the publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | GRICE LAB, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, GRICE LAB, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, GRICE LAB, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GC, GRICE EA, ET AL 2016. Script P3: Open Reading Frame Prediction. protocols.io dx.doi.org/10.17504/protocols.io.efpbbmn | 2021-03-29 03:10:31 | |
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Total RNA Purification from Plasma or Serum (ISOLATE II Biofluids RNA Kit) Resource Report Resource Website |
Bioline | 10.17504/protocols.io.f5hbq36 | Bioline | Protocol for RNA Purification form Plasma or Serum, using the ISOLATE II Biofluids RNA Kit. This protocol includes the lysate preparation procedure. | http://www.bioline.com/us/downloads/dl/file/id/3789/isolate_ii_biofluids_rna_kit_product_manual.pdf | 1 | 2016 | Bioline 2016. Total RNA Purification from Plasma or Serum (ISOLATE II Biofluids RNA Kit). protocols.io dx.doi.org/10.17504/protocols.io.f5hbq36 | 2021-03-29 03:10:31 | |||
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Transfection by Electroporation in Euplotes crassus Resource Report Resource Website |
Angela Piersanti | 10.17504/protocols.io.2a9gah6 | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Camerino | 2 | 2019 | Angela Piersanti 2019. Transfection by Electroporation in Euplotes crassus. protocols.io dx.doi.org/10.17504/protocols.io.2a9gah6 | 2021-03-29 03:10:28 | ||||
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Western Blot Resource Report Resource Website |
Payal Patel, Bethany Rozeboom, Tarah-Anne Abrigo | 10.17504/protocols.io.bfiijkce | Mercer University, Biochemistry Senior Capstone , Mercer University, Biochemistry Senior Capstone, Mercer University, Biochemistry Senior Capstone | 1 | 2020 | Payal Patel, Bethany Rozeboom, Tarah-Anne Abrigo 2020. Western Blot . protocols.io dx.doi.org/10.17504/protocols.io.bfiijkce | 2021-03-29 03:10:29 | |||||
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RNA re-precipitation protocol Resource Report Resource Website |
Cristian Riccio | 10.17504/protocols.io.3signce | If the RNA you have extracted is not pure and contains some residual contamination, as shown by poor Nanodrop ratios, you can reprecipitate the RNA, wash it and re-dissolve it to purify it. | Cancer Research UK / Wellcome Gurdon Institute | 2 | 2019 | Cristian Riccio 2019. RNA re-precipitation protocol. protocols.io dx.doi.org/10.17504/protocols.io.3signce | 2021-03-29 03:10:28 | ||||
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Imaging Mass Cytometry Modality Overview Resource Report Resource Website |
Michelle Daniel, Marda Jorgensen | 10.17504/protocols.io.bgatjsen | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | Unversity of Zurich, University of Florida | 2 | 2020 | Michelle Daniel, Marda Jorgensen 2020. Imaging Mass Cytometry Modality Overview . protocols.io dx.doi.org/10.17504/protocols.io.bgatjsen | 2021-03-29 03:10:27 | ||||
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PCR Using Q5® Hot Start High-Fidelity DNA Polymerase (M0493) Resource Report Resource Website |
New England Biolabs | 10.17504/protocols.io.cjtunm | New England Biolabs (NEB) | This protocols is for PCR using Q5® High-Fidelity DNA Polymerase (M0491) | New England Biolabs | https://www.neb.com/protocols/2012/08/30/pcr-using-q5-hot-start-high-fidelity-dna-polymerase-m0493 | 1 | 2015 | New England Biolabs 2015. PCR Using Q5® Hot Start High-Fidelity DNA Polymerase (M0493). protocols.io dx.doi.org/10.17504/protocols.io.cjtunm | 2021-03-29 03:10:27 | ||
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Effective Identification of Protein-Protein Interaction using RIME-IP Resource Report Resource Website |
George Laliotis | 10.17504/protocols.io.bqx8mxrw | The Ohio State University | 1 | 2020 | George Laliotis 2020. Effective Identification of Protein-Protein Interaction using RIME-IP. protocols.io dx.doi.org/10.17504/protocols.io.bqx8mxrw | 2021-03-29 03:10:30 | |||||
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One-step growth experiments (cyanophages) Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | 10.17504/protocols.io.dra52d | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Described is the procedure used to perform a onestep growth curve for cyanophage BBC1-P1 via plaque assay on Synechococcus sp. BBC1 (Suttle and Chan 1993). | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_118.pdf | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. One-step growth experiments (cyanophages). protocols.io dx.doi.org/10.17504/protocols.io.dra52d | 2021-03-29 03:10:29 | ||
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LyGo cloning Resource Report Resource Website |
Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Maja Rennig, Andreas Birk Bertelsen, Morten Norholm | 10.17504/protocols.io.bdmqi45w | Lytic polysaccharide monooxygenses (LPMOs) are enzymes that play a critical role in breaking the chemical bonds of the most abundant polymers found in recalcitrant biomass, such as cellulose and chitin. LyGo cloning (Lytic Polysaccharide Monooxygenase Golden Gate cloning) is a versatile heterologous expression platform for LPMOs, which is compatible with cloning both PCR products and synthetic gene fragments with a simple 15-minute assembly step. The method allows for parallel construction of multiple expression vectors, enabling exploration of several expression strategies. The open-source LyGo collection consists of vectors for some of the most relevant model organisms used for protein production in both academic and industrial settings.This protocol describes how to clone LyGo fragments into LyGo vectors. | Technical University of Denmark, Technical University of Denmark, Technical University of Denmark, Technical University of Denmark, Technical University of Denmark | 1 | 2020 | Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Maja Rennig, Andreas Birk Bertelsen, Morten Norholm 2020. LyGo cloning. protocols.io dx.doi.org/10.17504/protocols.io.bdmqi45w | 2021-03-29 03:10:30 | ||||
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UC Davis - HDL Protocol Resource Report Resource Website |
Peter Havel | 10.17504/protocols.io.ynsfvee | Mouse Metabolic Phenotyping Centers | LDL and VLDL are separated from HDL using a precipitation reagent. Then the HDL fraction is measured for either TC or TG using the same reagents for total cholesterol or triglyceride. | University of California, Davis | https://mmpc.org/shared/document.aspx?id=93&docType=Protocol | 1 | 2019 | Peter Havel 2019. UC Davis - HDL Protocol. protocols.io dx.doi.org/10.17504/protocols.io.ynsfvee | 2021-03-29 03:10:29 | ||
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MojoSort™ Streptavidin Nanobeads Protocol - Positive Selection Resource Report Resource Website |
Sam Li | 10.17504/protocols.io.7wghpbw | BioLegend | Product description and procedure summary:If your target cells are the labeled cells (the positive fraction), use the Streptavidin Nanobeads Protocol – Positive Selection. If your target cells are the unlabeled cells (negative fraction), use the Streptavidin Nanobeads Protocol - Negative Selection. Target cells are isolated by incubating your sample with a Biotin-conjugated antibody or antibody cocktail, followed by incubation with magnetic Streptavidin Nanobeads (Cat. No. 480015/480016). The magnetically labeled fraction is retained by the use of a magnetic separator. The untouched cells are collected. These are the cells of interest; do not discard the liquid. Some of the downstream applications include functional assays, gene expression, phenotypic characterization, etc.Note: This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube. If working with fewer than 107 cells, keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water. Scale up volumes if using 14 mL tubes and Magnet, and place the tube in the magnet for 10 minutes. | BioLegend | https://www.biolegend.com/protocols/mojosort-streptavidin-nanobeads-protocol-positive-selection/4748/ | 1 | 2019 | Sam Li 2019. MojoSort™ Streptavidin Nanobeads Protocol - Positive Selection. protocols.io dx.doi.org/10.17504/protocols.io.7wghpbw | 2021-03-29 03:10:28 | ||
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Painting Neuropixels probes and other silicon probes for electrophysiological recordings Resource Report Resource Website |
Liu Liu | 10.17504/protocols.io.wxqffmw | This protocol is for consistently applying fluorescent dyes to Neuropixels probes and other types of silicon probes, which allows imaging and reconstruction of the electrode tracks in the brain in post hoc histology. | Janelia Research Campus, HHMI | 1 | 2019 | Liu Liu 2019. Painting Neuropixels probes and other silicon probes for electrophysiological recordings. protocols.io dx.doi.org/10.17504/protocols.io.wxqffmw | 2021-03-29 03:10:30 |
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