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Validating that a specific subnetwork has significantly more interactions than expected by randomness Resource Report Resource Website |
Pascal Belleau, Astrid Deschênes, Martial Boutchueng-Djidjou, Robert L. Faure | DOI:10.17504/protocols.io.sdqea5w | Network science is a cross-disciplinary domain that focuses on the representation, analysis and modeling of complex systems as networks or graphs. In computational biology, Cytoscape is a very popular open source software platform for network modeling and visualization. As an example, Cytoscape can be used to identify disease modules which are defined as connected subnetworks showing mechanistic evidence for a specific phenotype.In the context of a new subnetwork identification, it is of interest to have access to measures of connectivity that help to assess the probability that this subnetwork could arise by chance.The R subnetsim package uses bootstrapping to test the hypothesis that a specific subnetwork is more connected than randomly generated subnetworks with the same number of nodes.Three measures of connectivity are validated by the R subnetsim package: - the number of nodes in the subnetwork including all the first-degree neighbor nodes - the number of links in the subnetwork including all the links of the first-degree neighbor nodes - the number of links in the subnetworkThe R subnetsim package also offers the possibility to easily graph the results of the simulations.This protocol provides the detailed method of a simulation analysis done on a specific subnetwork. To do so, the global subnetwork, from which the subnetwork is extracted, is needed in SIF format file. | Boutchueng-Djidjou M, Belleau P, Bilodeau N, Fortier S, Bourassa S, Droit A, Elowe S, Faure RL (2018) A type 2 diabetes disease module with a high collective influence for Cdk2 and PTPLAD1 is localized in endosomes. PLoS ONE 13(10): e0205180. doi: 10.1371/journal.pone.0205180 | Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory, H. Lee Moffit Cancer Center and Research Institut, Université Laval | https://doi.org/10.1371/journal.pone.0205180 | 1 | 2018 | Pascal Belleau, Astrid Deschênes, Martial Boutchueng-Djidjou, Robert L. Faure 2018. Validating that a specific subnetwork has significantly more interactions than expected by randomness. protocols.io https://dx.doi.org/10.17504/protocols.io.sdqea5w | 2021-04-15 09:15:51 | ||
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37°C heat shock survival assay for C. elegans Resource Report Resource Website |
Emily Troemel | DOI:10.17504/protocols.io.v6re9d6 | Reddy KC, Dror T, Underwood RS, Osman GA, Elder CR, Desjardins CA, Cuomo CA, Barkoulas M, Troemel ER (2019) Antagonistic paralogs control a switch between growth and pathogen resistance in C. elegans. PLoS Pathog 15(1): e1007528. doi: 10.1371/journal.ppat.1007528 | UCSD | https://doi.org/10.1371/journal.ppat.1007528 | 1 | 2018 | Emily Troemel 2018. 37°C heat shock survival assay for C. elegans. protocols.io https://dx.doi.org/10.17504/protocols.io.v6re9d6 | 2021-04-15 09:15:40 | |||
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Procedure for Operation and Maintenance of the Illumina MiSeq for Whole Genome Sequencing Resource Report Resource Website |
Julie Haendiges, Ruth Timme, Maria Balkey | DOI:10.17504/protocols.io.bja6kihe | GenomeTrakr | This procedure outlines the procedures for operation and maintenance of an Illumina MiSeq Sequencer for Whole Genoem Sequencing.This document applies to all laboratory personnel in the Division of Microbiology (DM) as well as laboratories in the GenomeTrakr Network.Complete in order:1. DNA Extraction (Manual DNA Extraction or Automated DNA Extraction using the Qiacube)Step-by-step procedures to obtain high quality DNA from isolates in TSB for whole genome sequencing2. DNA QuantitationQuantitation of extracted DNA using the Qubit Flourometer 3. Library Preparation for WGS (Library Preparation using Illumina DNA Prep or Library Preparation using Illumina Nextera XT )Library preparation using NexteraXT or Illumina DNA Prep (previously Nextera DNA Flex)2. DNA QuantitationQuantitation of extracted DNA using the Qubit Flourometer 3. Library Preparation for WGS (Library Preparation using Illumina DNA Prep or Library Preparation using Illumina Nextera XT )Library preparation using NexteraXT or Illumina DNA Prep (previously Nextera DNA Flex)3. Library Preparation for WGS (Library Preparation using Illumina DNA Prep or Library Preparation using Illumina Nextera XT )4. Sequencing using Illumina MiSeq (Included SOP)5. Data Quality Checks and NCBI Submission | US Food and Drug Administration, US Food and Drug Administration, US Food and Drug Administration | 1 | 2020 | Julie Haendiges, Ruth Timme, Maria Balkey 2020. Procedure for Operation and Maintenance of the Illumina MiSeq for Whole Genome Sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.bja6kihe | 2021-04-15 09:15:40 | |||
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Neural aggregate formation Resource Report Resource Website |
Celeste Karch, Rita Martinez, Jacob Marsh | DOI:10.17504/protocols.io.x84fryw | Neurodegeneration Method Development Community | Washington University in St Louis, Washington University in St Louis, Washington University in St Louis | 1 | 2019 | Celeste Karch, Rita Martinez, Jacob Marsh 2019. Neural aggregate formation. protocols.io https://dx.doi.org/10.17504/protocols.io.x84fryw | 2021-04-15 09:15:40 | ||||
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An analytical pipeline of assembly and annotation of the Betta splendens genome. Resource Report Resource Website |
Xin Liu | DOI:10.17504/protocols.io.qq9dvz6 | GigaScience Press, BGI | From here, You can learn about the detail methods of genome assembly and gene annotation of the Betta splendens genome. | BGI-Shenzhen | 1 | 2018 | Xin Liu 2018. An analytical pipeline of assembly and annotation of the Betta splendens genome.. protocols.io https://dx.doi.org/10.17504/protocols.io.qq9dvz6 | 2021-04-15 09:15:42 | |||
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Chemically competent E. coli cells Resource Report Resource Website |
Carlos Helbig | DOI:10.17504/protocols.io.psydnfw | This protocol describes how to make chemically competent Escherichia coli cell.For the protocol E. coli strain NEB Tubo was taken. | iGEM Marburg | 1 | 2018 | Carlos Helbig 2018. Chemically competent E. coli cells. protocols.io https://dx.doi.org/10.17504/protocols.io.psydnfw | 2021-04-15 09:15:42 | ||||
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RNAPath Target Identification via Fluorescent Hybridization Resource Report Resource Website |
Devin Willis | DOI:10.17504/protocols.io.bk37kyrn | XPRIZE Rapid Covid Testing, RNAPath | Scooter Willis | http://rnapath.com/ | 1 | 2020 | Devin Willis 2020. RNAPath Target Identification via Fluorescent Hybridization. protocols.io https://dx.doi.org/10.17504/protocols.io.bk37kyrn | 2021-04-15 09:15:55 | |||
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RNA Imaging with MERFISH - Imaging Resource Report Resource Website |
Jeffrey R. Moffitt, Xiaowei Zhuang | DOI:10.17504/protocols.io.mesc3ee | Human Cell Atlas Method Development Community, Neurodegeneration Method Development Community | The basic imaging process for MERFISH involves several fluid handling steps, e.g. introduction of hybridization buffers and wash and imaging buffers, in conjunction with the collection of smFISH images and the photobleaching of the sample. While it would be possible to perform these fluid exchange and imaging steps manually, we strongly recommend the use of an integrated and automated fluid exchange and imaging approach. Here we provide protocols for how to construct a fluid handling system that should be compatible with a variety of microscopes. We also discuss the basic protocols for hybridizing readout probes to samples on the microscope, imaging the sample, and bleaching residual signal. | Harvard University, Cambridge, Massachusetts, 02138 USA, Harvard University, Cambridge, Massachusetts, 02138 USA | https://www.ncbi.nlm.nih.gov/pubmed/27241748 | 1 | 2018 | Jeffrey R. Moffitt, Xiaowei Zhuang 2018. RNA Imaging with MERFISH - Imaging. protocols.io https://dx.doi.org/10.17504/protocols.io.mesc3ee | 2021-04-15 09:15:42 | ||
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Determination of protein levels of browning genes in murine adipose tissues by western blotting. Resource Report Resource Website |
Bianca Hemmeryckx, Dries Bauters, H. Roger Lijnen | DOI:10.17504/protocols.io.kbfcsjn | Increasing energy expenditure by stimulating thermogenesis through activation of brown adipose tissue (BAT) and/or induction of browning of white adipose tissue (WAT) is considered a promising strategy to treat/prevent obesity and related metabolic diseases. Whereas WAT is adapted to store energy as triglycerides, BAT produces heat (non-shivering thermogenesis). In brown adipocytes, the uncoupling protein-1 (Ucp-1) regulates conversion of energy into heat by uncoupling ATP production from mitochondrial respiration. Also in WAT adaptive Ucp-1 positive adipocytes (brown in white: brite or beige) can arise, predominantly in subcutaneous (s) WAT. Therefore, this browning of sWAT can be visualized by making sWAT protein extracts and by analyzing protein levels of brown adipocyte-specific markers such as Ucp-1 and peroxisome proliferator-activated receptor gamma coactivator 1 α (Pgc1α) in these extracts. | Bauters D, Bedossa P, Lijnen HR, Hemmeryckx B (2018) Functional role of ADAMTS5 in adiposity and metabolic health. PLoS ONE 13(1): e0190595. doi: 10.1371/journal.pone.0190595 | KU Leuven, KU Leuven, KU Leuven | https://doi.org/10.1371/journal.pone.0190595 | 1 | 2018 | Bianca Hemmeryckx, Dries Bauters, H. Roger Lijnen 2018. Determination of protein levels of browning genes in murine adipose tissues by western blotting.. protocols.io https://dx.doi.org/10.17504/protocols.io.kbfcsjn | 2021-04-15 09:15:43 | ||
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Pig- Heart Neuonal and Fiber Immunocytochemistry Resource Report Resource Website |
Pradeep Rajendran, John Tompkins, Kalyanam Shivkumar | DOI:10.17504/protocols.io.2n9gdh6 | SPARC | UCLA, UCLA, UCLA | 1 | 2019 | Pradeep Rajendran, John Tompkins, Kalyanam Shivkumar 2019. Pig- Heart Neuonal and Fiber Immunocytochemistry. protocols.io https://dx.doi.org/10.17504/protocols.io.2n9gdh6 | 2021-04-15 09:15:43 | ||||
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Whole-body clearing of beetles by successive treatment of hydrogen peroxide and CUBIC reagents Resource Report Resource Website |
Monto Kuroda, Shinya Kuroda | DOI:10.17504/protocols.io.ba33igqn | Optical Clearing of Tissue | Internal tissues of multicellular organisms cannot directly be seen because they contain pigments. For this reason, whole-body clearing methods have been developed and applied to mammals such as mice. Insects such as beetles, however, cannot be cleared by the mammalian method because of pigments such as melanin in their exoskeletons. In this study, we tried to develop a whole-body clearing method for large beetles. We first bleached the exoskeleton using a hydrogen peroxide treatment, and applied the the advanced Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis (CUBIC) reagents to make the internal tissues transparent. The combined method of hydrogen peroxide and the advanced CUBIC allowed us to successfully perform whole-body clearing of the large beetles. | Keika High school, l, 5-6-6 Hakusan, Bunkyo-ku, 112-8612, Tokyo, Japan, Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan | 1 | 2020 | Monto Kuroda, Shinya Kuroda 2020. Whole-body clearing of beetles by successive treatment of hydrogen peroxide and CUBIC reagents. protocols.io https://dx.doi.org/10.17504/protocols.io.ba33igqn | 2021-04-15 09:15:43 | |||
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T4 DNA Ligase Reaction Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.cf7trm | New England Biolabs (NEB) | This is the reaction for the "Ligation Protocol with T4 DNA Ligase" | New England Biolabs | https://www.neb.com/protocols/1/01/01/dna-ligation-with-t4-dna-ligase-m0202 | 1 | 2015 | New England Biolabs 2015. T4 DNA Ligase Reaction. protocols.io https://dx.doi.org/10.17504/protocols.io.cf7trm | 2021-04-15 09:15:55 | ||
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DIY Spin Column DNA Extraction Resource Report Resource Website |
Sarah Hessen-Schmidt | DOI:10.17504/protocols.io.fjtbknn | University of Southern California | 1 | 2016 | Sarah Hessen-Schmidt 2016. DIY Spin Column DNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.fjtbknn | 2021-04-15 09:15:42 | |||||
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PNGase F Mixture 1 Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.cqgvtv | New England Biolabs (NEB) | New England Biolabs | https://www.neb.com/protocols/2014/07/31/pngase-f-protocol | 1 | 2015 | New England Biolabs 2015. PNGase F Mixture 1. protocols.io https://dx.doi.org/10.17504/protocols.io.cqgvtv | 2021-04-15 09:15:55 | |||
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Chimeric Protein-LAG and Peptostreptococcal protein L sandwich ELISA Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.btbaniie | Carbon | This ELISA is used to study the interactions between protein-LAG (PLAG) and Peptostreptococcal protein-L (SpL) with different immunoglobulin preparations from mammalian and avian species. | University of the West Indies St. Augustine | 1 | 2021 | Angel Justiz-Vaillant 2021. Chimeric Protein-LAG and Peptostreptococcal protein L sandwich ELISA. protocols.io https://dx.doi.org/10.17504/protocols.io.btbaniie | 2021-04-15 09:15:44 | |||
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Protocols for Agarose Preparation Using Denville LE Agarose Resource Report Resource Website |
Denville Scientific | DOI:10.17504/protocols.io.gskbwcw | Denville Scientific, Inc. | Denville LE Agarose is an all purpose agarose for routine nucleic acid electrophoresis of fragments between 500bp-23,000 bp.Denville LE Agarose has no detectable DNase or RNase activity.Please refer to the appropriate protocol below, depending on whether you are using a hot plate or a microwave. | https://www.denvillescientific.com/products/agarose | 1 | 2016 | Denville Scientific 2016. Protocols for Agarose Preparation Using Denville LE Agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.gskbwcw | 2021-04-15 09:15:44 | |||
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QUESTIONNAIRE ABOUT ECO METHOD IMPLEMENTATION IN THE UNIVERSITY Resource Report Resource Website |
Juan Jesus Torres-Gordillo | DOI:10.17504/protocols.io.bhp5j5q6 | The purpose of this questionnaire is to know the impact of the implementation of the ECO method in the University. It is part of an innovation project, entitled ECO in Higher Education. Teaching inspired by the environment, funded by the University of Seville's 3rd Teaching Plan. It is intended for teachers who have been part of the innovation project. The data collected will be analysed to be used in the final report, as well as in some conference communications or journal articles.The questionnaire consists of 29 questions, divided into three blocks: 12 initial questions on demographic data, 9 closed-ended questions with four options and 8 open-ended questions. For open-ended questions, we ask that you answer in detail and as explicitly as possible.Each teacher is requested to complete one questionnaire per course in which they have implemented the ECO method. Similarly, if there have been two teachers in a shared course, each must fulfill, from their experience, a separate questionnaire.Thank you very much for your collaboration.Prof. Juan-Jesús Torres-GordilloUniversity of Seville (Spain) | Torres-Gordillo J, Melero-Aguilar N, García-Jiménez J (2020) Improving the university teaching-learning process with ECO methodology: Teachers’ perceptions. PLoS ONE 15(8): e0237712. doi: 10.1371/journal.pone.0237712 | Universidad de Sevilla | https://doi.org/10.1371/journal.pone.0237712 | 1 | 2020 | Juan Jesus Torres-Gordillo 2020. QUESTIONNAIRE ABOUT ECO METHOD IMPLEMENTATION IN THE UNIVERSITY. protocols.io https://dx.doi.org/10.17504/protocols.io.bhp5j5q6 | 2021-04-15 09:15:44 | ||
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Modified Bacterial Conjugation Protocol For Pseudo-nitzschia multiseries Resource Report Resource Website |
April Woods, G Jason Smith | DOI:10.17504/protocols.io.gj6bure | Protist Research to Optimize Tools in Genetics (PROT-G), Environmental Biotechnology Lab | This is a modified version of 'Conjugation of Thalassiosira pseudonana', publishedby J. Turnsek dx.doi.org/10.17504/protocols.io.f55bq86 .The protocol was modified to enhance viability in the diatom Pseudo-nitzschia multiseries. This version was used to transform Pseudo-nitzschia multiseries isolate 15091C3 with an episomal plasmid derived from pPtPUC3 to express a egfp gene under control of the P. multiseries actin promoter and termination domains. | Moss Landing Marine Labs, Moss Landing Marine Labs | 1 | 2017 | April Woods, G Jason Smith 2017. Modified Bacterial Conjugation Protocol For Pseudo-nitzschia multiseries. protocols.io https://dx.doi.org/10.17504/protocols.io.gj6bure | 2021-04-15 09:15:44 | |||
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Chlamydomonas reinhardtii nuclear transformation by electroporation. Resource Report Resource Website |
João Vitor Molino, Beth Rasala, Stephen Mayfield | DOI:10.17504/protocols.io.kfkctkw | This protocols describe the steps required for nuclear transformation of Chlamydomonas reinhardtii by electroporation. | Molino JVD, Carvalho JCMd, Mayfield SP (2018) Comparison of secretory signal peptides for heterologous protein expression in microalgae: Expanding the secretion portfolio for Chlamydomonas reinhardtii. PLoS ONE 13(2): e0192433. doi: 10.1371/journal.pone.0192433 | University of São Paulo, University of California, San Diego, University of California, San Diego | https://doi.org/10.1371/journal.pone.0192433 | 1 | 2018 | João Vitor Molino, Beth Rasala, Stephen Mayfield 2018. Chlamydomonas reinhardtii nuclear transformation by electroporation.. protocols.io https://dx.doi.org/10.17504/protocols.io.kfkctkw | 2021-04-15 09:15:44 | ||
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Unique insights from ClinicalTrials.gov by mining protein mutations and RSids in addition to applying the Human Phenotype Ontology Resource Report Resource Website |
Shray Alag | DOI:10.17504/protocols.io.bfacjiaw | Researchers and clinicians face a significant challenge in keeping up-to-date with the rapid rate of new associations between genetic mutations and diseases. To remedy this problem, this research mined the ClinicalTrials.gov corpus to extract relevant biological insights, produce unique reports to summarize findings, and make the meta-data available via APIs. An automated text-analysis pipeline performed the following features: parsing the ClinicalTrials.gov files, extracting and analyzing mutations from the corpus, mapping clinical trials to Human Phenotype Ontology (HPO), and finding associations between clinical trials and HPO nodes. Unique reports were created for each mutation (SNPs and protein mutations) mentioned in the corpus, as well as for each clinical trial that references a mutation. These reports, which have been run over multiple time points, along with APIs to access meta-data, are freely available on http://snpminertrials.com. Additionally, HPO was used to normalize disease terms and associate clinical trials with relevant genes. The creation of the pipeline and reports, the association of clinical trials with HPO terms, and the insights, public repository, and APIs produced are all novel in this work. The freely-available resources present relevant biological information and novel insights between biomedical entities in a robust and accessible manner, mitigating the challenge of being informed about new associations between mutations, genes, and diseases. | Alag S (2020) Unique insights from ClinicalTrials.gov by mining protein mutations and RSids in addition to applying the Human Phenotype Ontology. PLoS ONE 15(5): e0233438. doi: 10.1371/journal.pone.0233438 | The Harker School, San Jose | http://snpminertrials.com | 1 | 2020 | Shray Alag 2020. Unique insights from ClinicalTrials.gov by mining protein mutations and RSids in addition to applying the Human Phenotype Ontology. protocols.io https://dx.doi.org/10.17504/protocols.io.bfacjiaw | 2021-04-15 09:15:44 |
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