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Hemolysis Assay Resource Report Resource Website |
Noreen Wauford | DOI:10.17504/protocols.io.fxkbpkw | 1 | 2016 | Noreen Wauford 2016. Hemolysis Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.fxkbpkw | 2021-04-15 09:15:56 | ||||||
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4-methylumbelliferyl heptanoate (MUH) - Cell Viability Assay Resource Report Resource Website |
Peter Vangheluwe, Shaun Martin, Mujahid Azfar | DOI:10.17504/protocols.io.bazjif4n | The 4-methylumbelliferyl heptanoate (MUH) assay is a A fluorimetric assay used to study cell-mediated cytotoxicity. The principle behind this assay employs the activity of esterases found in viable cells. These esterases then hydolyse the fluorochrome in the MUH reagent which can then be read using a plate reader. | KU Leuven, KU Leuven, KU Leuven | 2 | 2020 | Peter Vangheluwe, Shaun Martin, Mujahid Azfar 2020. 4-methylumbelliferyl heptanoate (MUH) - Cell Viability Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.bazjif4n | 2021-04-15 09:15:56 | ||||
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Phusion HotStart II Hifi PCR Resource Report Resource Website |
Snehadri Sinha | DOI:10.17504/protocols.io.gzjbx4n | Aalto-Helsinki 2016 | PCR using Phusion HotStart II Hifi Mastermix (based on ThermoFisher Scientific manufacturer protocol). | 1 | 2017 | Snehadri Sinha 2017. Phusion HotStart II Hifi PCR. protocols.io https://dx.doi.org/10.17504/protocols.io.gzjbx4n | 2021-04-15 09:15:56 | ||||
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Methods and protocols from Goncalves et al. (2017) for manipulating the diet and the microbiome of Drosophila Resource Report Resource Website |
Zita Santos, Patrícia Francisco, Margarida Anjos, Célia Baltazar, Ana Paula Elias, Gabriela Tondolo Fioreze, Pavel M. Itskov, Matthew D. W. Piper, Carlos Ribeiro | DOI:10.17504/protocols.io.hdtb26n | Ribeiro Lab | This is a collection of methods and protocols from the manuscript: Gonçalves et al. Commensal bacteria and essential amino acids control food choice behavior and reproduction. Plos Biology. 2017 Apr 18. | Leitão-Gonçalves R, Carvalho-Santos Z, Francisco AP, Fioreze GT, Anjos M, Baltazar C, Elias AP, Itskov PM, Piper MDW, Ribeiro C (2017) Commensal bacteria and essential amino acids control food choice behavior and reproduction. PLoS Biol 15(4): e2000862. doi:10.1371/journal.pbio.2000862 | Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences, Champalimaud Centre for the Unknown, School of Biological Sciences | https://doi.org/10.1371/journal.pbio.2000862 | 1 | 2017 | Zita Santos, Patrícia Francisco, Margarida Anjos, Célia Baltazar, Ana Paula Elias, Gabriela Tondolo Fioreze, Pavel M. Itskov, Matthew D. W. Piper, Carlos Ribeiro 2017. Methods and protocols from Goncalves et al. (2017) for manipulating the diet and the microbiome of Drosophila. protocols.io https://dx.doi.org/10.17504/protocols.io.hdtb26n | 2021-04-15 09:15:56 | |
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Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization Resource Report Resource Website |
Bei Wang, Daniel Asarnow, Wen-Hsin Lee, Ching-Wen Huang, Bryan Faust, Patricia Miang Lon Ng, Eve Zi Xian Ngoh, Markus Bohn, David Bulkley, Andrés Pizzorno, Hwee Ching Tan, Chia-Yin Lee, Rabiatul Adawiyah Minhat, Olivier Terrier, Mun Kuen Soh, Frannie Jiuyi Teo, Yvonne Yee Chin Yeap, Yuanyu Hu, Shirley Gek Kheng Seah, Sebastian Maurer-Stroh, Laurent Renia, Brendon John Hanson, Manuel Rosa-Calatrava, Aashish Manglik, Yifan Cheng, Charles S. Craik, Cheng-I Wang | DOI:10.17504/protocols.io.bi35kgq6 | Coronavirus Method Development Community | In vitro antibody selection against pathogens from naïve combinatorial libraries can yield various classes of antigen-specific binders that are distinct from those evolved from natural infection. Also, rapid neutralizing antibody discovery can be made possible by a strategy that selects for those interfering with pathogen and host interaction. Here we report the discovery of antibodies that neutralize SARS-CoV-2, the virus responsible for the COVID-19 pandemic, from a highly diverse naïve human Fab library. Lead antibody 5A6 blocks the receptor binding domain (RBD) of the viral spike from binding to the host receptor angiotensin converting enzyme 2 (ACE2), neutralizes SARS-CoV-2 infection of Vero E6 cells, and reduces viral replication in reconstituted human nasal and bronchial epithelium models. 5A6 has a high occupancy on the viral surface and exerts its neutralization activity via a bivalent binding mode to the tip of two neighbouring RBDs at the ACE2 interaction interface, one in the “up” and the other in the “down” position, explaining its superior neutralization capacity. Furthermore, 5A6 is insensitive to several spike mutations identified in clinical isolates, including the D614G mutant that has become dominant worldwide. Our results suggest that 5A6 could be an effective prophylactic and therapeutic treatment of COVID-19. | Singapore Immunology Network, A*STAR, Singapore, Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, USA; QBI COVID-19 Research Group (QCRG), San Francisco, USA, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, USA; QBI COVID-19 Research Group (QCRG), San Francisco, USA, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, QBI COVID-19 Research Group (QCRG), San Francisco, USA; Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, USA, Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, USA; QBI COVID-19 Research Group (QCRG), San Francisco, USA, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Lyon, France, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Lyon, France, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore, Biological Defence Program, DSO National Laboratories, Singapore, Bioinformatics Institute, A*STAR, Singapore, Singapore Immunology Network, A*STAR, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore; Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Biological Defence Program, DSO National Laboratories, Singapore, Centre International de Recherche en Infectiologie (CIRI), Université de Lyon, Lyon, France; VirNext, Faculté de Médecine RTH Laennec, Université de Lyon, Lyon, France, QBI COVID-19 Research Group (QCRG), San Francisco, USA; Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, USA; Department of Anesthesia and Perioperative Care, University of California San Francisco (UCSF), San Francisco, USA, Department of Biochemistry and Biophysics, University of California San Francisco (UCSF) School of Medicine, San Francisco, USA; QBI COVID-19 Research Group (QCRG), San Francisco, USA; Howard Hughes Medical Institute, University of California San Francisco (UCSF), San Francisco, USA, QBI COVID-19 Research Group (QCRG), San Francisco, USA; Department of Pharmaceutical Chemistry, University of California San Francisco (UCSF), San Francisco, USA, Singapore Immunology Network, A*STAR, Singapore | https://www.biorxiv.org/content/10.1101/2020.07.14.203414v1?rss=1 | 1 | 2020 | Bei Wang, Daniel Asarnow, Wen-Hsin Lee, Ching-Wen Huang, Bryan Faust, Patricia Miang Lon Ng, Eve Zi Xian Ngoh, Markus Bohn, David Bulkley, Andrés Pizzorno, Hwee Ching Tan, Chia-Yin Lee, Rabiatul Adawiyah Minhat, Olivier Terrier, Mun Kuen Soh, Frannie Jiuyi Teo, Yvonne Yee Chin Yeap, Yuanyu Hu, Shirley Gek Kheng Seah, Sebastian Maurer-Stroh, Laurent Renia, Brendon John Hanson, Manuel Rosa-Calatrava, Aashish Manglik, Yifan Cheng, Charles S. Craik, Cheng-I Wang 2020. Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization. protocols.io https://dx.doi.org/10.17504/protocols.io.bi35kgq6 | 2021-04-15 09:15:56 | ||
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UC Davis - Microvascular Permeability and Lipoprotien Flux Resource Report Resource Website |
John Rutledge | DOI:10.17504/protocols.io.56vg9e6 | Mouse Metabolic Phenotyping Centers | One of the three indices of arterial function that are compromised to a varying degree in individuals with cardiovascular disease is vascular permeability. This assay measures vascular permeability (as flux of labeled large molecular weight molecules: i.e. albumin or dextran) and lipid permeability (as flux of labeled lipid) in coronary or carotid arteries. | University of California, Davis | https://mmpc.org/shared/document.aspx?id=108&docType=Protocol | 2 | 2019 | John Rutledge 2019. UC Davis - Microvascular Permeability and Lipoprotien Flux. protocols.io https://dx.doi.org/10.17504/protocols.io.56vg9e6 | 2021-04-15 09:15:56 | ||
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Measuring specific leaf area and water content Resource Report Resource Website |
Etienne Laliberté | DOI:10.17504/protocols.io.p3tdqnn | Plant Functional Ecology Lab, Canadian Airborne Biodiversity Observatory | Here we describe the standardised protocol used by the Canadian Airborne Biodiversity Observatory (CABO) to measure leaf water content and specific leaf area, using the WinFOLIA™ software (Régent Instruments). These leaf area and water measurements are done on a subset of leaves from the same bulk leaf sample used to measure leaf spectral reflectance and transmittance. Briefly, after removing their petioles, fresh leaves are weighed, rehydrated for 6 h, scanned for total leaf area and weighed again; they are then oven-dried at 65 ºC for 72 h, and weighed one last time. This allows us to measure leaf dry matter content and its complement, leaf water content, as well as leaf relative water content. Leaf area measurements are used to estimate specific leaf area, a key functional trait central to the leaf economics spectrum. Specific leaf area allows us to estimate equivalent water thickness and to convert concentrations of foliar biochemical constitutents from a leaf mass to a leaf area basis. | Université de Montréal | 1 | 2018 | Etienne Laliberté 2018. Measuring specific leaf area and water content. protocols.io https://dx.doi.org/10.17504/protocols.io.p3tdqnn | 2021-04-15 09:15:56 | |||
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CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers Resource Report Resource Website |
Peter J. Skene, Steven Henikoff | DOI:10.17504/protocols.io.mgjc3un | Human Cell Atlas Method Development Community | Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing. As only the targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has exceptionally low background levels. CUT&RUN outperforms the most widely used Chromatin Immunoprecipitation (ChIP) protocols in resolution, signal-to-noise, and depth of sequencing required. In contrast to ChIP, CUT&RUN is free of solubility and DNA accessibility artifacts and can be used to profile insoluble chromatin and to detect long-range 3D contacts without cross-linking. Here we present an improved CUT&RUN protocol that does not require isolation of nuclei and provides high-quality data starting with only 100 cells for a histone modification and 1000 cells for a transcription factor. From cells to purified DNA CUT&RUN requires less than a day at the lab bench.In summary, CUT&RUN has several advantages over ChIP-seq: (1) The method is performed in situ in non-crosslinked cells and does not require chromatin fragmentation or solubilization; (2) The intrinsically low background allows low sequence depth and identification of low signal genomic features invisible to ChIP; (3) The simple procedure can be completed within a day and is suitable for robotic automation; (4) The method can be used with low cell numbers compared to existing methodologies; (5) A simple spike-in strategy can be used for accurate quantitation of protein-DNA interactions. As such, CUT&RUN represents an attractive replacement for ChIPseq, which is one of the most popular methods in biological research. | Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington, USA 98109, Howard Hughes Medical Institute, Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington, USA 98109 | https://www.biorxiv.org/content/early/2017/09/24/193219 | 1 | 2018 | Peter J. Skene, Steven Henikoff 2018. CUT&RUN: Targeted in situ genome-wide profiling with high efficiency for low cell numbers. protocols.io https://dx.doi.org/10.17504/protocols.io.mgjc3un | 2021-04-15 09:15:59 | ||
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During data acquisition Resource Report Resource Website |
Lukas Snoek, Tinka Beemsterboer | DOI:10.17504/protocols.io.ypwfvpe | Spinoza Centre, REC-L | This protocol lists all the steps necessary to run your MRI experiment/data acquisition safely and in a way that yields high-quality data. Moreover, if you use the centre's QC/preprocessing service, it lists the steps necessary to make sure we can convert the data into BIDS and run them through the QC/preprocessing pipelines. | Spinoza Centre, REC-L, Spinoza Centre, REC-L | 10 | 2019 | Lukas Snoek, Tinka Beemsterboer 2019. During data acquisition. protocols.io https://dx.doi.org/10.17504/protocols.io.ypwfvpe | 2021-04-15 09:15:56 | |||
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Fig 9. Effect of installation distance of shakers on weight on bit and accelerations of the drill-string. A. Change of weight on bit in the bottom hole over time. B. Maximum acceleration along the drill-string. C. Root mean square acceleration along the dr Resource Report Resource Website |
Peng Wang, Hongjian Ni, Ruihe Wang | DOI:10.17504/protocols.io.kfactie | Wang P, Ni H, Wang R (2018) A new drilling method—Earthworm-like vibration drilling. PLoS ONE 13(4): e0194582. doi: 10.1371/journal.pone.0194582 | China University of Petroleum, China University of Petroleum, China University of Petroleum | https://doi.org/10.1371/journal.pone.0194582 | 1 | 2018 | Peng Wang, Hongjian Ni, Ruihe Wang 2018. Fig 9. Effect of installation distance of shakers on weight on bit and accelerations of the drill-string. A. Change of weight on bit in the bottom hole over time. B. Maximum acceleration along the drill-string. C. Root mean square acceleration along the dr. protocols.io https://dx.doi.org/10.17504/protocols.io.kfactie | 2021-04-15 09:15:57 | |||
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Quantitative Real‐Time Polymerase Chain Reaction (qRT‐PCR) Resource Report Resource Website |
Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying | Neurodegeneration Method Development Community | Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology; Hugo W. Moser Research Institute at Kennedy Krieger, Department of Physiology and Biophysics, Howard University, College of Life Sciences, Northwest University, Department of Neurology, Johns Hopkins University School of Medicine; Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine; Adrienne Helis Malvin Medical Research Foundation, Hugo W. Moser Research Institute at Kennedy Krieger; Department of Neurology, Johns Hopkins University School of Medicine, Department of Neurology, Johns Hopkins University School of Medicine; Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine; Adrienne Helis Malvin Medical Research Foundation; Department of Neuroscience, Johns Hopkins University School of Medicine; Department of Physiology, Johns Hopkins University School of Medicine, Department of Neurology, Johns Hopkins University School of Medicine; Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine; Adrienne Helis Malvin Medical Research Foundation; Department of Neuroscience, Johns Hopkins University School of Medicine; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Hugo W. Moser Research Institute at Kennedy Krieger; Department of Neurology, Johns Hopkins University School of Medicine; Department of Neuroscience, Johns Hopkins University School of Medicine; Department of Oncology, Johns Hopkins University School of Medicine, Department of Immunology, Research Center on Pediatric Development and Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, State Key Laboratory of Medical Molecular Biology, Hugo W. Moser Research Institute at Kennedy Krieger; Department of Neurology, Johns Hopkins University School of Medicine | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6344911/ | 1 | 2020 | Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying 2020. Quantitative Real‐Time Polymerase Chain Reaction (qRT‐PCR). protocols.io https:// | 2021-04-15 09:15:51 | ||||
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4% Formaldehyde in .1M PB (FOR IMMUNO BRAINS) (1L) Resource Report Resource Website |
Molly Brennan, Olivier George | George Lab | University of California, San Diego, University of California, San Diego | 1 | 2020 | Molly Brennan, Olivier George 2020. 4% Formaldehyde in .1M PB (FOR IMMUNO BRAINS) (1L). protocols.io https:// | 2021-04-15 09:15:51 | |||||
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Cas9 RNP nucleofection for cell lines using Lonza 4D Nucleofector Resource Report Resource Website |
Mark Dewitt & Julia Wong | DOI:10.17504/protocols.io.hd8b29w | Innovative Genomics Institute, CornLab | This protocol, based on published work, demonstrates how to delivery Cas9 RNP-based gene editing reagents to cultured mamallian cells by electroporation with a Lonza 4d Nucleofector. Consider consulting some of the following papers:1. RNP delivery paper upon which this work is based (Open Access):https://elifesciences.org/content/3/e047662. Paper by an IGI post-doc that details the rationale behind HDR donor design:https://www.ncbi.nlm.nih.gov/pubmed/26789497 | 3 | 2017 | Mark Dewitt & Julia Wong 2017. Cas9 RNP nucleofection for cell lines using Lonza 4D Nucleofector. protocols.io https://dx.doi.org/10.17504/protocols.io.hd8b29w | 2021-04-15 09:15:51 | ||||
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Blocking Solution (Donkey) Resource Report Resource Website |
Sonia Hall | DOI:10.17504/protocols.io.fevbje6 | University of Massachusetts Medical School | 1 | 2016 | Sonia Hall 2016. Blocking Solution (Donkey). protocols.io https://dx.doi.org/10.17504/protocols.io.fevbje6 | 2021-04-15 09:15:57 | |||||
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RNA clean-up by phenol:chloroform Resource Report Resource Website |
Daniel Richter | DOI:10.17504/protocols.io.8y3hxyn | Phenol: chloroform extraction to clean up RNA ( e.g. to remove DNAse or DNAse Inactivation Reagent.) Based on phenol/chloroform protocol (http://cshprotocols.cshlp.org/content/2010/6/pdb.prot5438.full), ethanol precipitation protocol (http://cshprotocols.cshlp.org/content/2010/6/pdb.prot5440.full) | King Lab, University of California Berkeley | https://elifesciences.org/articles/34226 | 2 | 2019 | Daniel Richter 2019. RNA clean-up by phenol:chloroform. protocols.io https://dx.doi.org/10.17504/protocols.io.8y3hxyn | 2021-04-15 09:15:51 | |||
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Epidural morphine combined with single-injection femoral nerve block for postoperative analgesia in patients after total knee arthroplasty: a randomized controlled trial Resource Report Resource Website |
Zhao-Ting Meng, Fan Cui, Xue-Ying Li, Dong-Xin Wang | DOI:10.17504/protocols.io.wanfade | Total knee arthroplasty (TKA) is an important therapy for patients with serious knee osteoarthritis in order to improve quality of life and relieve pain. But a large number of patients who undergo this surgery experience moderate to severe postoperative pain. Previously, the investigators used single femoral nerve blockade combined with patient-controlled intravenous analgesia for postoperative analgesia for patients after TKA. Although this method provides acceptable analgesia, the incidence of opioid-associated side effects is relatively high. Low-dose epidural morphine is commonly used in postoperative analgesia after cesarean section, and the effect of single dose morphine lasts more than 20 hours, with low incidences of itching, nausea, vomiting, and respiratory depression. The investigators hypothesize that, for patients undergoing TKA, the addition of low-dose epidural morphine to single femoral nerve block and intravenous opioids can improve the postoperative analgesia, reduce the consumption of intravenous opioids and decrease opioid-associated side effects. | Meng Z, Cui F, Li X, Wang D (2019) Epidural morphine improves postoperative analgesia in patients after total knee arthroplasty: A randomized controlled trial. PLoS ONE 14(7): e0219116. doi: 10.1371/journal.pone.0219116 | Peking University First Hospital, Peking University First Hospital, Peking University First Hospital, Peking University First Hospital | https://doi.org/10.1371/journal.pone.0219116 | 2 | 2018 | Zhao-Ting Meng, Fan Cui, Xue-Ying Li, Dong-Xin Wang 2018. Epidural morphine combined with single-injection femoral nerve block for postoperative analgesia in patients after total knee arthroplasty: a randomized controlled trial. protocols.io https://dx.doi.org/10.17504/protocols.io.wanfade | 2021-04-15 09:15:57 | ||
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Two-step protocol: Preparation and extrusion of phospholipid liposomes Resource Report Resource Website |
James Collins, James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy | DOI:10.17504/protocols.io.zbef2je | Van Mooy Lab @ WHOI | The protocols in this collection were original created by Krista Longnecker and Jamie Collins for creating lipsomes to be used in lipid photo-oxidation experiments. The results of these experiments are detailed in:Collins, J. R, H. F. Fredricks, J. S. Bowman, C. P. Ward, C. Moreno, K. Longnecker, A. Marchetti, C. M. Hansel, H. W. Ducklow, and B. A. S. Van Mooy. 2018. The molecular products and biogeochemical significance of lipid photooxidation in West Antarctic surface waters. Geochimica et Cosmochimica Acta 232:244–264; doi:10.1016/j.gca.2018.04.030and in Chapter 4 of:Collins, J. R. 2017. The remineralization of marine organic matter by diverse biological and abiotic processes. Ph.D. thesis. Cambridge, Massachusetts: Massachusetts Institute of Technology, 300 pp; doi:10.1575/1912/8721 | Oregon Department of Environmental Quality, Woods Hole Oceanographic Institution, Woods Hole Oceanographic Institution, Woods Hole Oceanographic Institution, Woods Hole Oceanographic Institution | https://doi.org/10.1016/j.gca.2018.04.030 | 3 | 2019 | James Collins, James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy 2019. Two-step protocol: Preparation and extrusion of phospholipid liposomes. protocols.io https://dx.doi.org/10.17504/protocols.io.zbef2je | 2021-04-15 09:15:51 | ||
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BGISEQ-500 Sequencing Resource Report Resource Website |
Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao | DOI:10.17504/protocols.io.pq7dmzn | GigaScience Press, BGI, GIGA, GigaScience Press | BGISEQ-500 is a new desktop sequencer developed by BGI. Using DNA nanoball and combinational probe anchor synthesis developed from Complete Genomics™ sequencing technologies, it generates short reads at a large scale. | Huang J, Liang X, Xuan Y, Geng C, Li Y, Lu H, Qu S, Mei X, Chen H, Yu T, Sun N, Rao J, Wang J, Zhang W, Chen Y, Liao S, Jiang H, Liu X, Yang Z, Mu F, Gao S, Erratum to: A reference human genome dataset of the BGISEQ-500 sequencer. GigaScience 7(12). doi: 10.1093/gigascience/giy144 | National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, State Food and Drug Administration, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC), State Food and Drug Administration, National Institutes for Food and Drug Control (NIFDC), National Institutes for Food and Drug Control (NIFDC), National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, BGI-Qingdao, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC), BGI-Shenzhen, National Institutes for Food and Drug Control (NIFDC) | https://doi.org/10.1093/gigascience/giy144 | 1 | 2018 | Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao 2018. BGISEQ-500 Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.pq7dmzn | 2021-04-15 09:15:51 | |
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nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon) Resource Report Resource Website |
Nikki Freed, Olin Silander | DOI:10.17504/protocols.io.bfwnjpde | Coronavirus Method Development Community | To enable faster, easier sequencing of SARS-COV2 genomes with fewer steps than current methods, we use multiplexed 1200 base pair PCR amplicons with the Oxford Nanopore RAPID barcoding kit (RBK004). This is a modification of the ARTIC amplicon V3 sequencing protocol for MinION for nCoV-2019 developed by Josh Quick, which produces 400 base pair amplicons and uses the Oxford Nanopore Ligation barcoding kit (LSK-109). We have increased the size of the amplicons to 1200bp and use the RAPID barcode kit (RBK004), which enables requires less time and fewer reagents than the LSK-109 protocol. The amplicons produced in this protocol could also be used for Illumina sequencing. Primers were all designed using Primal Scheme: http://primal.zibraproject.org/, described here https://www.nature.com/articles/nprot.2017.066.Primer sequences are here: https://docs.google.com/spreadsheets/d/1M5I_C56ZC8_2Ycgm9EFieVlVNqxsP7dXAnGoBZy3nDo/edit?usp=sharingWe can ship a small amount of pooled primers to interested labs for further testing, email [email protected] or [email protected] | Massey University, Massey University | 1 | 2020 | Nikki Freed, Olin Silander 2020. nCoV-2019 sequencing protocol (RAPID barcoding, 1200bp amplicon). protocols.io https://dx.doi.org/10.17504/protocols.io.bfwnjpde | 2021-04-15 09:15:51 | |||
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Ultracentrifuge clean-up of phage lysate for TEM Resource Report Resource Website |
Kathy Lam | University of California, San Francisco | 1 | 2020 | Kathy Lam 2020. Ultracentrifuge clean-up of phage lysate for TEM. protocols.io https:// | 2021-04-15 09:15:51 |
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