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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Focus group methodology for Doctor Who viewing behaviors Resource Report Resource Website |
Hannah Gunderman | DOI:10.17504/protocols.io.bjjykkpw | This protocol is a description of how Hannah Gunderman facilitates her focus groups around Doctor Who episodes in order to better understand how viewers perceive messages of empathy, geography, and social themes in the episodes. In this example, Hannah describes her focus group protocol for the Doctor Who episode "Vincent and the Doctor" (Series 5, episode 10). This protocol is meant to demonstrate how the protocols.io platform can be used to document workflows and methods within humanities researcher, showing how the platform can be for any researcher regardless of domain area. | Carnegie Mellon University | 1 | 2020 | Hannah Gunderman 2020. Focus group methodology for Doctor Who viewing behaviors . protocols.io https://dx.doi.org/10.17504/protocols.io.bjjykkpw | 2021-04-15 09:15:38 | ||||
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Flongle DirectRNA Library preparation Resource Report Resource Website |
Maximilian Krause | DOI:10.17504/protocols.io.bcwcixaw | The Nordic Nanopore-Seq Network | Oxford Nanopore Technologies allows sequencing of native RNA for the first time. Additionally they released tiny devices that democratize sequencing among scientists. However, the smallest sequencing device - Flongle - is so far not officially supported for RNA sequencing experiments.This protocol provides users with a personally tested framework protocol to use Flongle flow-cells for native RNA sequencing. It is based on the protocol for ONT RNA library preparation and changed to fit the volume and input requirements for Flongle.The here advised workflow will routinely result in 100,000 native RNA reads within 24 hours of sequencing. | University of Bergen | http://doi:10.1261/rna.071332.119 | 1 | 2020 | Maximilian Krause 2020. Flongle DirectRNA Library preparation. protocols.io https://dx.doi.org/10.17504/protocols.io.bcwcixaw | 2021-04-15 09:15:53 | ||
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RAT-ChIP - Restriction Assisted Tagmentation Chromatin Immunoprecipitation Resource Report Resource Website |
Tonis Org, Kati Hensen, Rita Kreevan, Elina Mark, Olav Sarv, Reidar Andreson, Ülle Jaakma, Andres Salumets, Ants Kurg | DOI:10.17504/protocols.io.69qhh5w | Chromatin immunoprecipitation coupled with next-generation sequencing (ChIP-seq) has revolutionized our understanding of chromatin-related biological processes. The method, however, requires thousands of cells and has therefore limited applications in situations where cell numbers are limited. Here we describe a novel method called Restriction Assisted Tagmentation Chromatin Immunoprecipitation (RAT-ChIP) that enables global histone modification profiling from as few as 100 cells. The method is simple, cost-effective and takes a single day to complete. | Org T, Hensen K, Kreevan R, Mark E, Sarv O, Andreson R, Jaakma | Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia, Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia, Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia, Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia., Competence Centre on Health Technologies, Tartu, Estonia, Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Institute of Genomics, University of Tartu, Tartu, Estonia, Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia., Competence Centre on Health Technologies, Tartu, Estonia; Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia; Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia; Department of Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland., Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia | https://doi.org/10.1371/journal.pone.0225801 | 1 | 2019 | Tonis Org, Kati Hensen, Rita Kreevan, Elina Mark, Olav Sarv, Reidar Andreson, Ülle Jaakma, Andres Salumets, Ants Kurg 2019. RAT-ChIP - Restriction Assisted Tagmentation Chromatin Immunoprecipitation . protocols.io https://dx.doi.org/10.17504/protocols.io.69qhh5w | 2021-04-15 09:15:35 | ||
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Western Blot Sample Prep- Whole Drosophila Embryos Resource Report Resource Website |
Sonia Hall | DOI:10.17504/protocols.io.cnzvf5 | University of Massachusetts Medical School | 1 | 2015 | Sonia Hall 2015. Western Blot Sample Prep- Whole Drosophila Embryos. protocols.io https://dx.doi.org/10.17504/protocols.io.cnzvf5 | 2021-04-15 09:15:36 | |||||
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Small-scale silencing experiment in vegetative Euplotes crassus (provisional) Resource Report Resource Website |
Rachele Cesaroni | DOI:10.17504/protocols.io.hi5b4g6 | Protist Research to Optimize Tools in Genetics (PROT-G) | Universität Bern | 4 | 2017 | Rachele Cesaroni 2017. Small-scale silencing experiment in vegetative Euplotes crassus (provisional). protocols.io https://dx.doi.org/10.17504/protocols.io.hi5b4g6 | 2021-04-15 09:15:35 | ||||
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ECOGEO 'Omics Training: 4.2 Annotation Resource Report Resource Website |
Rekha Seshadri | DOI:10.17504/protocols.io.fi8bkhw | ECOGEO | Introduction to functional annotation and Integrated Microbial Genomes (IMG) at the Joint Genome Institute (JGI).Open this protocol inside the virtual machine (details in 'Start Instructions') for easy copy, paste of commands into the command line terminal window. | EarthCube Oceanography and Geobiology Environmental 'Omics | 2 | 2016 | Rekha Seshadri 2016. ECOGEO 'Omics Training: 4.2 Annotation. protocols.io https://dx.doi.org/10.17504/protocols.io.fi8bkhw | 2021-04-15 09:15:35 | |||
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this is a test Resource Report Resource Website |
Anita Bandrowski | DOI:10.17504/protocols.io.2g9gbz6 | RRID:AB_90755 | SciCrunch Inc and UCSD | 1 | 2020 | Anita Bandrowski 2020. this is a test. protocols.io https://dx.doi.org/10.17504/protocols.io.2g9gbz6 | 2021-04-15 09:15:35 | ||||
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BG-11 Trace metal mix A5 Resource Report Resource Website |
Dr. Steven Wilhelm | DOI:10.17504/protocols.io.h92b98e | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol. | 2 | 2017 | Dr. Steven Wilhelm 2017. BG-11 Trace metal mix A5. protocols.io https://dx.doi.org/10.17504/protocols.io.h92b98e | 2021-04-15 09:15:35 | ||||
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UC Davis - Metabolomics: Sample preparation for Lipidomics Resource Report Resource Website |
Oliver Fiehn | DOI:10.17504/protocols.io.ytpfwmn | Mouse Metabolic Phenotyping Centers, Metabolomics Protocols & Workflows | Summary:This SOP describes sample extraction and sample preparation for lipid profiling by liquid chromatography / quadrupole time of flight mass spectrometry (LC-QTOF) or nanoelectrospray ion trap-FTICR MS. | University of California, Davis | https://mmpc.org/shared/document.aspx?id=122&docType=Protocol | 1 | 2019 | Oliver Fiehn 2019. UC Davis - Metabolomics: Sample preparation for Lipidomics. protocols.io https://dx.doi.org/10.17504/protocols.io.ytpfwmn | 2021-04-15 09:15:36 | ||
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Removal of gDNA from totalRNA Resource Report Resource Website |
Igem Dusseldorf | DOI:10.17504/protocols.io.8bfhsjn | Removal of genomic DNA from RNA preparations | Heinrich-Heine Universität Düsseldorf | 1 | 2019 | Igem Dusseldorf 2019. Removal of gDNA from totalRNA. protocols.io https://dx.doi.org/10.17504/protocols.io.8bfhsjn | 2021-04-15 09:15:34 | ||||
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Protein A- Protein A Sandwich ELISA Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bsu4neyw | This ELISA was used to study Staphylococcal protein-A (SpA) interactions with various mammalian and avian immunoglobulins. | University of the West Indies St. Augustine | 1 | 2021 | Angel Justiz-Vaillant 2021. Protein A- Protein A Sandwich ELISA. protocols.io https://dx.doi.org/10.17504/protocols.io.bsu4neyw | 2021-04-15 09:15:34 | ||||
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CTTI Pregnancy Testing in Clinical Trials Project Survey Resource Report Resource Website |
Sara Calvert | DOI:10.17504/protocols.io.rj6d4re | The main purpose of pregnancy testing as part of a clinical research protocol is to minimize risk to an embryo or fetus from exposure to potentially harmful study interventions. The specific goal of testing may be to prevent exposure completely (by testing prior to any study interventions), or to minimize the duration of exposure during early pregnancy (by periodic testing during the study).This survey provided five clinical study scenarios and asked respondents a series of questions about the acceptable risk of an unintended fetal exposure to a drug, the importance of several factors going into clinical study design, and the type of pregnancy testing protocol that you would recommend. | Morse JE, Calvert SB, Jurkowski C, Tassinari M, Sewell CA, Myers ER (2018) Evidence-based pregnancy testing in clinical trials: Recommendations from a multi-stakeholder development process. PLoS ONE 13(9): e0202474. doi: 10.1371/journal.pone.0202474 | Duke University | https://doi.org/10.1371/journal.pone.0202474 | 1 | 2018 | Sara Calvert 2018. CTTI Pregnancy Testing in Clinical Trials Project Survey. protocols.io https://dx.doi.org/10.17504/protocols.io.rj6d4re | 2021-04-15 09:15:34 | ||
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HTAPP_NST- Nuclei isolation from frozen tissue Resource Report Resource Website |
Eugene Drokhlyansky, Nicholas Van Wittenberghe, Michal Slyper, Julia Waldman, Asa Segerstolpe, Orit Rozenblatt-Rosen, Aviv Regev | DOI:10.17504/protocols.io.bhbdj2i6 | NCIHTAN | This protocol describes a nuclei isolation method for frozen tissues based on the previously published protocol by Gao et al. and modified by Drokhlyansky et al. It can be used on both healthy and disease tissues and is compatible with droplet-based single-nucleus RNA-Seq technology Slyper et al.This method is part of a toolbox for processing frozen tissue samples for single-nucleus RNA-Seq, including the NST (this protocol), CST and TST protocols (all available in protocols.io). We recommend users to test all three protocols on their tissue type of interest and perform side-by-side comparison of the data generated. A description of the complete toolbox and guidance for testing and selecting methods from the toolbox for processing other tumors can be found in Slyper et al.For the Human Tumor Atlas Pilot Project (HTAPP), this protocol was tested on metastatic breast cancer, ovarian cancer and pediatric neuroblastoma frozen samples. For these cancer types, however, TST was the protocol of choice. When tested on HTAPP samples, NST, in general, underperformed compared to TST and CST based on several QC parameters. | Broad Institute;Human Tumor Atlas Pilot Project, Broad Institute;Human Tumor Atlas Pilot Project, Broad Institute;Human Tumor Atlas Pilot Project, Broad Institute;Human Tumor Atlas Pilot Project, Broad Institute;Human Tumor Atlas Pilot Project, Broad Institute;Human Tumor Atlas Pilot Project, Broad Institute;Human Tumor Atlas Pilot Project;Massachusetts Institute of Technology;Howard Hughes Medical Institute | 2 | 2020 | Eugene Drokhlyansky, Nicholas Van Wittenberghe, Michal Slyper, Julia Waldman, Asa Segerstolpe, Orit Rozenblatt-Rosen, Aviv Regev 2020. HTAPP_NST- Nuclei isolation from frozen tissue. protocols.io https://dx.doi.org/10.17504/protocols.io.bhbdj2i6 | 2021-04-15 09:15:34 | |||
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Wuhan coronavirus (2019-nCoV) real-time RT-PCR ORF1ab 2020 (Wuhan-ORF1ab) Resource Report Resource Website |
Judy Northill, Ian Mackay | DOI:10.17504/protocols.io.bbsginbw | protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services | A real-time RT-PCR to detect the "novel Wuhan" betacoronavirus or Wuhan seafood market pneumonia virus. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region is within the ORF1ab sequence.Not tested on wild-type virus (as of 25Jan2020), it is expected to be capable of only detecting the Wuhan coronavirus.NotesAssay is fully optimised (as of 24Jan2020).A final name for this virus has not been decided (as of 25Jan2020). | Public Health Virology, Forensic and Scientific Services, Public Health Virology, Forensic and Scientific Services | 1 | 2020 | Judy Northill, Ian Mackay 2020. Wuhan coronavirus (2019-nCoV) real-time RT-PCR ORF1ab 2020 (Wuhan-ORF1ab). protocols.io https://dx.doi.org/10.17504/protocols.io.bbsginbw | 2021-04-15 09:15:34 | |||
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Building an HPC blast pipeline Resource Report Resource Website |
Bonnie Hurwitz | DOI:10.17504/protocols.io.d5a82d | Hurwitz Lab, ABE487_HMP, ABE487_EMP | This tutorial shows you how to create a pipeline on the University of Arizona HPC. Specifically, we will be creating a pipeline to run blast, using scripts you are writing or have already written from ABE 487 weeks 10 and 11. The pipeline will do the following:1. split each of the files from the night/day transcriptome into files with 10,000 sequences each2. run blastp against uniprot_sprot.fasta3. parse the blast results | University of Arizona | 1 | 2015 | Bonnie Hurwitz 2015. Building an HPC blast pipeline. protocols.io https://dx.doi.org/10.17504/protocols.io.d5a82d | 2021-04-15 09:15:34 | |||
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Multi-Seq: my notes from the lab Resource Report Resource Website |
Luciano Martelotto | DOI:10.17504/protocols.io.bejyjcpw | A1Please note these are just my notes and by no means are ground truth of how Multi-seq needs to be performed. I WELCOME to comments, suggestions and amendments. | Harvard Medical School | 1 | 2020 | Luciano Martelotto 2020. Multi-Seq: my notes from the lab. protocols.io https://dx.doi.org/10.17504/protocols.io.bejyjcpw | 2021-04-15 09:15:35 | ||||
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Sample preparation protocol for hair fiber curvature analysis Resource Report Resource Website |
Tina Lasisi | DOI:10.17504/protocols.io.bbweipbe | This protocol prepares hair fibers per sample for curvature analysis.Diagrams were created with BioRender.com | Pennsylvania State University | https://tinalasisi.github.io/2020_HairPheno_manuscript/index.html | 1 | 2020 | Tina Lasisi 2020. Sample preparation protocol for hair fiber curvature analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.bbweipbe | 2021-04-15 09:15:51 | |||
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Find Proteins of Unknown Function (PUFs) using Plantannot - Protocol C Resource Report Resource Website |
Marcos Viana, Mauricio Mudadu, Adhemar Zerlotini | DOI:10.17504/protocols.io.bgdijs4e | A1The Plantannot software provides several filters and a text search box that allows searching for molecules by its desired annotation features. These filters are needed to obtain PUFs and to try to relate them to abiotic stresses using RNA-seq expression data and co-expression networks. The Filters menu is separated in 8 fields, of those we are going to use only five: “Organism”, “Feature type”, “Orthology”, “Orthologs_coexpression” and “Analyses”. The “Feature Type” filter has three molecule types, from those the polypeptide box is the only that is going to be always checked and the others blank. By using the other 4 remaining filters, 6 protocols were created as examples of different ways to selecting PUFs. Protocol A: using lack of both homology and protein domain signatures. Protocol B: using lack of homology, presence of domain signatures - trying to select Domains of Unknown Function (DUF) from PFAM, and the text search “Unknown function”.Protocol C: using homology, lack of protein domain signatures and the text search “Unknown function”. Protocol D-F: same protocols of A-C but using ortholog groups to find homolog proteins with co-expression data related to abiotic stress.2Protocol C is intended do find PUFs from organisms that proteins are already public in the NCBI´s nr database and have no protein domains found by Interproscan. Proteins will be selected using the text search "Unknown function". | EMBRAPA, EMBRAPA, EMBRAPA | https://www.machado.cnptia.embrapa.br/plantannot | 1 | 2020 | Marcos Viana, Mauricio Mudadu, Adhemar Zerlotini 2020. Find Proteins of Unknown Function (PUFs) using Plantannot - Protocol C. protocols.io https://dx.doi.org/10.17504/protocols.io.bgdijs4e | 2021-04-15 09:15:51 | |||
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Centrifuged Sample Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ddj24m | VERVE Net, Sullivan Lab | For One-step growth curves for Cellulophaga phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Centrifuged Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ddj24m | 2021-04-15 09:15:35 | |||
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Western Blot CTB Resource Report Resource Website |
Arindam Naha | DOI:10.17504/protocols.io.bastieen | For studying intracellular accumulation of CTB subunits in E coli, bacteria were grown up to 4 hours following induction by 0.2% of arabinose. Post induction, bacterial cultures were mixed with equal volume of translation-translocation halt cocktail (200 µg/ml chloramphenicol, 200 mM sodium azide, 9.5% ethanol) and immediately placed in an ice water bath for 15 minutes of incubation to arrest protein synthesis and translocation. Cells were harvested by centrifugation at 14000 rpm for 15 minutes at 4°C. Supernatants were preserved and used for CT-ELISA experiment as described before. Pellets were then suspended in TME buffer (20 mM Tris-Cl pH 8.0, 2mM β-mercaptoethanol, 1 mM EDTA), preferably 1/10th volume of the original culture and disrupted by sonication. After centrifugation at 13,000 rpm at 4°C for 15 min to remove any unbroken cells, crude cell lysates were used for measurement of protein concentration using Bradford assay (BioRad, USA). Equal amount (≥80 μg) of protein samples were mounted on to 15% SDS-PAGE. Blots were probed with classical CTB-specific monoclonal antibody (anti-Cla CTB, 1:5000) or anti-beta lactamase (anti-βla 1:500) antibody. A portion of the same blot was stained with Ponceau S staining solution (Sigma-Aldrich, St Louis, MO, USA) to validate whether equal amount protein samples were transferred in the blot. Blots were developed using West Pico Chemiluminescent Substrate (Thermo Scientific, Rockford, IL) according to the manufacturer’s instructions and visualized in ChemiDoc XRS+ system (BioRad, USA). Densitometric analysis of band intensities was performed using the Multi Gauge software V2.3(FujiFilm). .justify:after { content: ""; display:inline-block; width: 100%; } | Naha A, Mandal RS, Samanta P, Saha RN, Shaw S, Ghosh A, Chatterjee NS, Dutta P, Okamoto K, Dutta S, Mukhopadhyay AK (2020) Deciphering the possible role of ctxB7 allele on higher production of cholera toxin by Haitian variant Vibrio cholerae O1. PLoS Negl Trop Dis 14(4): e0008128. doi: 10.1371/journal.pntd.0008128 | Post Doctoral Fellow, Indian Institute of Science (Previously Ph.D Student. National Institute of Cholera and Enteric Diseases) | https://doi.org/10.1371/journal.pntd.0008128 | 1 | 2019 | Arindam Naha 2019. Western Blot CTB. protocols.io https://dx.doi.org/10.17504/protocols.io.bastieen | 2021-04-15 09:15:51 |
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