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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Kings B Media (1L) Resource Report Resource Website |
Brian Smith, [email protected] Micro.tucson | 10.17504/protocols.io.xf4fjqw | University of Arizona, University of Arizona | 1 | 2019 | Brian Smith, [email protected] Micro.tucson 2019. Kings B Media (1L). protocols.io dx.doi.org/10.17504/protocols.io.xf4fjqw | 2021-03-29 03:10:13 | |||||
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BGISEQ-500 （DNBSEQ-G50） 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 | 10.17504/protocols.io.bimzkc76 | BGI | 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. | 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 | 2020 | 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 2020. BGISEQ-500 （DNBSEQ-G50） Sequencing. protocols.io dx.doi.org/10.17504/protocols.io.bimzkc76 | 2021-03-29 03:10:11 | ||
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Centrifuge the whole blood to separate red blood cells Resource Report Resource Website |
George Lykotrafitis | 10.17504/protocols.io.zzwf77e | Centrifuge the whole blood in order to obtain the red blood cells. | University of Connecticut | 1 | 2019 | George Lykotrafitis 2019. Centrifuge the whole blood to separate red blood cells. protocols.io dx.doi.org/10.17504/protocols.io.zzwf77e | 2021-03-29 03:10:11 | ||||
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Single Gel system based in Ahn T et al (2001) Resource Report Resource Website |
Luisa F. Jiménez Soto | 10.17504/protocols.io.gipbudn | This protocol was standarized in our lab based on the publication of Ahn T et al (2001): Polyacrylamide Gel Electrophoresis without a stacking Gel: Use of Amino Acids as Electrolytes. DOI:10.1006/abio.2001.5038 These gels run similar to a gradient gel: In a 6% gel you will be able to separate proteins ranging from 270 kDa to 25 kD an dhave them in the same gel.The adaptation to Stain-Free system was done based on the publication by Ladner CL et al (2004) : Visible fluorescent detection of proteins in polyacrylamide gels without staining. DOI:10.1016/j.ab.2003.10.047We have applied this protocol in the following publications: Zeitler AF, Gerrer KH, Haas R, Jiménez-Soto LF. Optimized semi-quantitative blot analysis in infection assays using the Stain-Free technology. J Microbiol Methods. 2016 Jul;126:38-41. doi: 10.1016/j.mimet.2016.04.016. PubMed PMID: 27150675.Jiménez-Soto LF, Haas R. The CagA toxin of Helicobacter pylori: abundant production but relatively low amount translocated. Sci Rep. 2016 Mar 17;6:23227. doi: 10.1038/srep23227. PubMed PMID: 26983895; PubMed Central PMCID: PMC4794710.Jiménez-Soto LF, Clausen S, Sprenger A, Ertl C, Haas R. Dynamics of the Cag-type IV secretion system of Helicobacter pylori as studied by bacterial co-infections. Cell Microbiol. 2013 Nov;15(11):1924-37. doi: 10.1111/cmi.12166. PubMed PMID: 23844976. | Behrens I, Busch B, Ishikawa-Ankerhold H, Palamides P, Shively JE, Stanners C, Chan C, Leung N, Gray-Owen S, Haas R, The HopQ-CEACAM Interaction Controls CagA Translocation, Phosphorylation, and Phagocytosis of in Neutrophils. mBio 11(1). doi: 10.1128/mBio.03256-19 | Max von Pettenkofer Institute - LMU Munich-Germany | https://doi.org/10.1371/journal.ppat.1007359 | 1 | 2016 | Luisa F. Jiménez Soto 2016. Single Gel system based in Ahn T et al (2001). protocols.io dx.doi.org/10.17504/protocols.io.gipbudn | 2021-03-29 03:10:11 | ||
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Laser Microdissection (LMD) for Regional Proteomics Resource Report Resource Website |
Samir Parikh, John Shapiro, Brad Rovin | 10.17504/protocols.io.brrqm55w | KPMP | Recent advances in multi-scale interrogation of human tissue, including advanced imaging techniques and the powerful application of large dataset “omics”, have displayed significant promise toward identifying new and specific therapeutic targets, predicting disease progression, and individualizing treatment in participants with acute and chronic kidney disease. Our site, formed by the alliance of Indiana University and Ohio State University, will implement an unbiased tissue interrogation workflow for KPMP human kidney biopsies that integrates largescale 3D tissue imaging for quantitative supervised and unsupervised analysis/cytometry with sub-segmental “omics” data on the same kidney biopsy specimen. The sub-segmental “omics” pipeline will use fluorescence based Laser MicroDissection (LMD) to isolate specific nephron segments and interstitial/other targeted areas, for downstream analysis with transcriptomics and proteomics. The omics analysis will be eventually expanded to include bulk epigenetics. Acting harmoniously with other KPMP sites, our interrogation techniques are expected to facilitate back-mapping of key molecular pathways to the biopsy, which can subsequently identify foci of injury and/or regeneration that can undergo targeted sampling to generate further enriched omics. Therefore, in addition to a significant contribution to the human kidney atlas, our approach will complement other interrogation techniques within KPMP by providing tissue context and increasing spatial resolution for molecular signatures that arise in heterogeneous areas during kidney disease. | Department of Medicine, Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA, Department of Medicine, Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA, Department of Medicine, Division of Nephrology, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA | 1 | 2021 | Samir Parikh, John Shapiro, Brad Rovin 2021. Laser Microdissection (LMD) for Regional Proteomics. protocols.io dx.doi.org/10.17504/protocols.io.brrqm55w | 2021-03-29 03:10:11 | |||
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Standardized immunohistochemical staining used in the Human Protein Atlas Resource Report Resource Website |
Anna Martinez Casals, Cecilia Lindskog | 10.17504/protocols.io.yj8furw | Human Protein Atlas | The Human Protein Atlas provides a map showing the distribution and relative abundance of proteins in the human body. All IHC staining in the Human Protein Atlas project are performed using the following standard protocol. The primary antibody dilution is based on titration optimization, the dilution suggested by the Human Protein Atlas can be found under antibody and antigen information for each antibody. When primary antibody originates from other host animals than rabbit, there are some modifications and different secondary antibody is used. | Science for Life Lab / Science for life laboratory / KTH - Royal Institute of Technology, Science for Life Lab / Science for life laboratory / KTH - Royal Institute of Technology | https://www.ncbi.nlm.nih.gov/pubmed/22688270 | 1 | 2019 | Anna Martinez Casals, Cecilia Lindskog 2019. Standardized immunohistochemical staining used in the Human Protein Atlas. protocols.io dx.doi.org/10.17504/protocols.io.yj8furw | 2021-03-29 03:10:11 | ||
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Electroporation of Heterosigma akashiwo Resource Report Resource Website |
Deepak Nanjappa and Kathryn Coyne | 10.17504/protocols.io.4qggvtw | This protocol was developed for transformation of Heterosigma akashiwo by electroporation. This species does not grow on solid medium, so transformants are grown "in bulk" and should not be considered clonal. We have had limited success with this protocol, which may need to be further optimized. | University of Delaware | 3 | 2019 | Deepak Nanjappa and Kathryn Coyne 2019. Electroporation of Heterosigma akashiwo. protocols.io dx.doi.org/10.17504/protocols.io.4qggvtw | 2021-03-29 03:10:12 | ||||
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XPRIZE SANATA Protocol for Saliva LFIA Test Resource Report Resource Website |
Mario Thomas, Jasmine Sollen, Natalia Ivanova, Michelle Feng, Reda Fayek, Heidi Abdilla, Stephanie Lim, Amanda Naaum | 10.17504/protocols.io.bqfrmtm6 | Coronavirus Method Development Community, XPRIZE Rapid Covid Testing, SANATA | This procedure outlines the protocol for testing for SARS-CoV-2 using a saliva sample collected from an individual. The purpose of this test is to detect low levels of SARS-CoV-2 antigen at a higher sensitivity. Precision Biomonitoring Inc. developed an ultra-rapid digital, disposable, highly-sensitive and inexpensive testing device used for screening purposes. The mobile app complementary to this medical device is connected through Bluetooth. Using this innovation, the user can be tested at point-of-care (POC) by a health care professional, and obtain qualitative results. | Precision Biomonitoring Inc., Precision Biomonitoring Inc., Precision Biomonitoring Inc., Precision Biomonitoring Inc., Precision Biomonitoring Inc., Precision Biomonitoring Inc., Precision Biomonitoring Inc., Precision Biomonitoring Inc. | 3 | 2020 | Mario Thomas, Jasmine Sollen, Natalia Ivanova, Michelle Feng, Reda Fayek, Heidi Abdilla, Stephanie Lim, Amanda Naaum 2020. XPRIZE SANATA Protocol for Saliva LFIA Test. protocols.io dx.doi.org/10.17504/protocols.io.bqfrmtm6 | 2021-03-29 03:10:14 | |||
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Chimeric Protein-LAG and Staphylococcal Protein A sandwich ELISA Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.btbbniin | Carbon | This ELISA was used to study the interactions between protein-LAG (PLAG) and staphylococcal protein-A (SpA) with different immunoglobulin preparations of mammalian and avian species. | University of the West Indies St. Augustine | 1 | 2021 | Angel Justiz-Vaillant 2021. Chimeric Protein-LAG and Staphylococcal Protein A sandwich ELISA. protocols.io dx.doi.org/10.17504/protocols.io.btbbniin | 2021-03-29 03:10:12 | |||
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Script R16: CRISPR Analysis Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | 10.17504/protocols.io.ejqbcmw | VERVE Net, Club Grice | This protocol outlines how to generate tables to analyze CRISPR interactions. Based on methods from the following 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 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script R16: CRISPR Analysis. protocols.io dx.doi.org/10.17504/protocols.io.ejqbcmw | 2021-03-29 03:10:12 | |
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DNA extraction for HMW DNA Resource Report Resource Website |
Natalie Solonenko, Marie Burris | 10.17504/protocols.io.6cbhasn | Sullivan Lab, Temperton Lab | This protocol is intended for extraction of HMW DNA from bacterial or viral samples. | The Ohio State University Department of Microbiology, The Ohio State University Department of Microbiology | 1 | 2019 | Natalie Solonenko, Marie Burris 2019. DNA extraction for HMW DNA. protocols.io dx.doi.org/10.17504/protocols.io.6cbhasn | 2021-03-29 03:10:11 | |||
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Superoxide Radical-scavenging Activity Resource Report Resource Website |
Jing Xu | 10.17504/protocols.io.bdaxi2fn | The superoxide radical scavenging effects were examined [11]. Briefly, extract (1 ml) was added to 1 ml of 50 μM NBT solution and 1 ml of 468 μMNADH, and a 1ml aliquot of 60 μM PMS reaction mixture. After 5min, absorbance was read at 560 nm. The inhibition percent and IC50 valueswere calculated. | Zhou J, Yang Q, Zhu X, Lin T, Hao D, Xu J (2020) Antioxidant activities of Clerodendrum cyrtophyllum Turcz leaf extracts and their major components. PLoS ONE 15(6): e0234435. doi: 10.1371/journal.pone.0234435 | Hainan University | https://doi.org/10.1371/journal.pone.0234435 | 1 | 2020 | Jing Xu 2020. Superoxide Radical-scavenging Activity. protocols.io dx.doi.org/10.17504/protocols.io.bdaxi2fn | 2021-03-29 03:10:14 | ||
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0.1 M Millonig's phosphate buffer (pH=7.2) Resource Report Resource Website |
Diogo Provete | 10.17504/protocols.io.e3vbgn6 | 1 | 2016 | Diogo Provete 2016. 0.1 M Millonig's phosphate buffer (pH=7.2). protocols.io dx.doi.org/10.17504/protocols.io.e3vbgn6 | 2021-03-29 03:10:14 | ||||||
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Testing antibacterial activity of bacteriophages on hard surfaces Resource Report Resource Website |
Elisabetta Caselli, Elisabetta Caselli | 10.17504/protocols.io.nwmdfc6 | Testing antibacterial activity of bacteriophages on hard surfaces | University of Ferrara, University of Ferrara | 1 | 2018 | Elisabetta Caselli, Elisabetta Caselli 2018. Testing antibacterial activity of bacteriophages on hard surfaces. protocols.io dx.doi.org/10.17504/protocols.io.nwmdfc6 | 2021-03-29 03:10:12 | ||||
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Phenol extraction of Chlorella cells Resource Report Resource Website |
David Dunigan and Irina Agarkova | 10.17504/protocols.io.eshbeb6 | VERVE Net | University of Nebraska-Lincoln | http://www.lclane.net/text/chlorellaphenol.html | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Phenol extraction of Chlorella cells. protocols.io dx.doi.org/10.17504/protocols.io.eshbeb6 | 2021-03-29 03:10:12 | |||
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2. Steps of Clinical Reasoning Process and Variables of Quality Indicators for Physiotherapy Care Process of Patients with WAD for Analysis Resource Report Resource Website |
Rob A B Oostendorp | 10.17504/protocols.io.utgewjw | Appendix 2.Overview of 9 Steps of Clinical Reasoning Process including the Variables of Quality Indicators for Physiotherapy Care Process of Patients with Whiplash-Associated Disorders (WAD) for Analysis | Scientific Institute for Quality of Healthcare (IQ healthcare), Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands | 2 | 2018 | Rob A B Oostendorp 2018. 2. Steps of Clinical Reasoning Process and Variables of Quality Indicators for Physiotherapy Care Process of Patients with WAD for Analysis. protocols.io dx.doi.org/10.17504/protocols.io.utgewjw | 2021-03-29 03:10:12 | ||||
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LessTests Resource Report Resource Website |
Ruth Polachek, doreen | 10.17504/protocols.io.bkiakuae | XPRIZE Rapid Covid Testing | LessTests SARS-CoV2 general diagnosis protocol, using LessTests software solution.The LessTests method is agnostic to the labware, and has already been demonstrated as successful using multiple device and kit combinations. | LessTests, LessTests | 1 | 2020 | Ruth Polachek, doreen 2020. LessTests. protocols.io dx.doi.org/10.17504/protocols.io.bkiakuae | 2021-03-29 03:10:13 | |||
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Seamless editing of sgRNAs cloning mixture Resource Report Resource Website |
Alexandre Paix | 10.17504/protocols.io.dxb7im | Genetics | http://www.genetics.org/content/198/4/1347.full | 1 | 2015 | Alexandre Paix 2015. Seamless editing of sgRNAs cloning mixture. protocols.io dx.doi.org/10.17504/protocols.io.dxb7im | 2021-03-29 03:10:13 | ||||
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Preparation of Binding Buffer (BB) Resource Report Resource Website |
Nicola O'Reilly, Svend Kjaer, Maria Greco | 10.17504/protocols.io.bfd2ji8e | Coronavirus Method Development Community, Crick COVID-19 Consortium | Purpose of examination / Clinical relevanceAt the end of 2019, several pneumonia cases were reported in Wuhan, China and the pathogen was confirmed as a new viral strain. World Health organization has named the newly identified coronavirus as 2019-nCoV, also known as COVID19. The disease developed into a dangerous pandemic, posing major challenges to the NHS. Although more research is necessary to better understand the virus, in response to the emergency, simple and rapid testing is essential to identify the virus in infected individuals. This will aid the implementation of efficient interventions to contain the spread, and distinguish healthcare workers who have been infected, and are required to self-isolate, from those showing similar symptoms but which are not 2019-nCoV associated. The latter category may continue to work, alleviating stress on hard-pressed healthcare resources. 2019-nCoV is an RNA virus, and the diagnostic tests detect viral RNA in swabs from patient airways using a reverse transcriptase PCR assay. Samples are submitted to HSL, an accredited reporting laboratory, and transferred to FCI for testing.Principles of ExaminationThis procedure involves the preparation of binding buffer for the RNA extraction protocol. |
Aitken, J., Ambrose, K., Barrell, S. et al. Scalable and robust SARS-CoV-2 testing in an academic center. Nat Biotechnol (2020). https://doi.org/10.1038/s41587-020-0588-y |
The Francis Crick Institute, The Francis Crick Institute, The Francis Crick Institute | https://doi.org/10.1038/s41587-020-0588-y | 1 | 2020 | Nicola O'Reilly, Svend Kjaer, Maria Greco 2020. Preparation of Binding Buffer (BB). protocols.io dx.doi.org/10.17504/protocols.io.bfd2ji8e | 2021-03-29 03:10:13 | |
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SYSB 3036 W01: Introduction to Unix Resource Report Resource Website |
Frank Aylward | 10.17504/protocols.io.xhffj3n | Virginia Tech | 2 | 2019 | Frank Aylward 2019. SYSB 3036 W01: Introduction to Unix. protocols.io dx.doi.org/10.17504/protocols.io.xhffj3n | 2021-03-29 03:10:14 |
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