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| Name | Authors | DOI | Group |
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RRIDs used | ||||||
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Metatranscriptomic screening for genes of interest Resource Report Resource Website |
Helena Pound, Steven Wilhelm | DOI:10.17504/protocols.io.7vyhn7w | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Great Lakes Center for Fresh Waters and Human Health | Find genes of interest in assembled metatranscriptomic library using blast. | University of Tennessee, Knoxville, The University of Tennessee, Knoxville | http://wilhelmlab.utk.edu/ | 1 | 2019 | Helena Pound, Steven Wilhelm 2019. Metatranscriptomic screening for genes of interest. protocols.io https://dx.doi.org/10.17504/protocols.io.7vyhn7w | 2021-04-15 09:14:23 | ||
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CRAC Analysis in Budding Yeast with HTP Tagged Proteins Resource Report Resource Website |
Rosey Bayne, Stefan Bresson, David Tollervey, Edward Wallace | DOI:10.17504/protocols.io.5ppg5mn | Wallace lab for Fungal RNA | CRAC (Cross-linking and cDNA Analysis) is a method that uses UV-crosslinking to identify which RNAs bind to an RNA-Binding Protein of interest and the specific sites in the RNA where this binding occurs. CRAC is one of the family of UV crosslinking and immunoprecipitation (CLIP) protocols, reviewed by Lee and Ule (DOI: 0.1016/j.molcel.2018.01.005).The protein is tagged with with a tandem affinity tag: in this protocol we use an HTP tag (His6-TEV-ProteinA) that allows immuno-affinity purification of the protein with its cross-linked RNAs by binding of the ProteinA moiety of the tag to IgG Sepharose columns. After washing, the protein is then released from the column by cleavage with TEV protease and subjected to nickel-affinity purification through the His6 moiety under highly denaturing conditions. This allows accurate mapping of RNA binding sites (Bohnsack, et al, DOI: 10.1016/B978-0-12-396546-2.00013-9) ; Granneman, S. et al (DOI: 10.1073/pnas.0901997106 ). The protocol can also be adapted for use with HTF (His6-TEV-FLAG3) tags (Tree, J.J. et al, DOI: 10.1016/j.molcel.2014.05.006) or HF (His8-Ala4-FLAG) tags (Bresson, S., Shchepachev, V., Spanos, C., Turowski, T., Rappsilber, J. and Tollervey, D.(2020): DOI: /10.1101/2020.05.14.096354) by replacing the IgG sepharose column with anti-FLAG magnetic beads and elution with excess FLAG peptide, removing the need for TEV cleavage which can be inefficient. The cDNA libraries generated allow a transcriptome -wide analysis of the interactome of the protein. | School of Biological Sciences, University of Edinburgh, Wellcome Centre for Cell Biology, University of Edinburgh, Wellcome Centre for Cell Biology, University of Edinburgh, School of Biological Sciences, University of Edinburgh | 1 | 2020 | Rosey Bayne, Stefan Bresson, David Tollervey, Edward Wallace 2020. CRAC Analysis in Budding Yeast with HTP Tagged Proteins. protocols.io https://dx.doi.org/10.17504/protocols.io.5ppg5mn | 2021-04-15 09:14:26 | |||
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Ebola virus sequencing protocol Resource Report Resource Website |
Josh Quick | DOI:10.17504/protocols.io.7nwhmfe | ARTIC | University of Birmingham | 1 | 2019 | Josh Quick 2019. Ebola virus sequencing protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7nwhmfe | 2021-04-15 09:14:29 | ||||
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Reverse transcription of complementary DNA Resource Report Resource Website |
Madeline M Glennon, Austin Skinner, Mara Krutsinger, Marino Resendiz | DOI:10.17504/protocols.io.birskd6e | Glennon MM, Skinner A, Krutsinger M, Resendiz MJE (2020) Translesion synthesis by AMV, HIV, and MMLVreverse transcriptases using RNA templates containing inosine, guanosine, and their 8-oxo-7,8-dihydropurine derivatives. PLoS ONE 15(8): e0235102. doi: 10.1371/journal.pone.0235102 | University of Colorado Denver, University of Colorado Denver, University of Colorado Denver, University of Colorado Denver | https://doi.org/10.1371/journal.pone.0235102 | 1 | 2020 | Madeline M Glennon, Austin Skinner, Mara Krutsinger, Marino Resendiz 2020. Reverse transcription of complementary DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.birskd6e | 2021-04-15 09:14:29 | |||
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Original dataset Resource Report Resource Website |
Ji Won Choi, Duk Kyung Kim, Jin Kyoung Kim, Eun Jee Lee, Jea Youn Kim | DOI:10.17504/protocols.io.mbyc2pw | Original dataset of the study entitled "A retrospective analysis on the relationship between intraoperative hypothermia and postoperative ileus after laparoscopic colorectal surgery" | Samsung Medical Center, Republic of Korea, , , , | 1 | 2017 | Ji Won Choi, Duk Kyung Kim, Jin Kyoung Kim, Eun Jee Lee, Jea Youn Kim 2017. Original dataset. protocols.io https://dx.doi.org/10.17504/protocols.io.mbyc2pw | 2021-04-15 09:14:29 | ||||
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Monterey Wharf II Cell Enumeration For HABMAP Reporting Resource Report Resource Website |
April Woods, G Jason Smith | DOI:10.17504/protocols.io.pcbdisn | Cell preservation and counting techniques for Monterey Wharf II monitoring and CA-HABMAP reporting. | Moss Landing Marine Labs, Moss Landing Marine Laboratories | 1 | 2018 | April Woods, G Jason Smith 2018. Monterey Wharf II Cell Enumeration For HABMAP Reporting. protocols.io https://dx.doi.org/10.17504/protocols.io.pcbdisn | 2021-04-15 09:14:29 | ||||
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Intestinal Organoid Dissociation and Nuclei Isolation for Single Cell ATAC-Seq Resource Report Resource Website |
Heather Eckart, Ran Zhou | DOI:10.17504/protocols.io.bdeui3ew | Helmsley project_Basu lab | This protocol provides a procedure for human intestinal organoid dissociation into a single cell suspension and nuclei isolation prior to Single Cell ATAC-Sequencing. | University of Chicago, University of Chicago | 1 | 2020 | Heather Eckart, Ran Zhou 2020. Intestinal Organoid Dissociation and Nuclei Isolation for Single Cell ATAC-Seq. protocols.io https://dx.doi.org/10.17504/protocols.io.bdeui3ew | 2021-04-15 09:14:23 | |||
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Cloning of L0 parts into pUAP-ye for Loop typeIIS Resource Report Resource Website |
Eftychis Frangedakis, Susana Sauret-Gueto | DOI:10.17504/protocols.io.4wdgxa6 | OpenPlant Project | University of Cambridge, Plant Sciences, University of Cambridge, OpenPlant | 1 | 2019 | Eftychis Frangedakis, Susana Sauret-Gueto 2019. Cloning of L0 parts into pUAP-ye for Loop typeIIS. protocols.io https://dx.doi.org/10.17504/protocols.io.4wdgxa6 | 2021-04-15 09:14:23 | ||||
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Assembly Instructions for colosseum Resource Report Resource Website |
Sina Booeshaghi, Yeokyoung Kil, Kyung Hoi Min, Jase Gehring, Lior Pachter | DOI:10.17504/protocols.io.btz3np8n | Pachter Lab | We present colosseum, a low-cost, modular, and automated fluid sampling device for scalable fluidic applications. The colosseum fraction collector uses a single motor, can be built for less than $100 using off-the-shelf and 3D-printed components, and can be assembled in less than an hour. Build Instructions and source files are available at https://github.com/pachterlab/colosseum. | Department of Mechanical Engineering, California Institute of Technology, Pasadena, California, Department of Medical Engineering, California Institute of Technology, Pasadena, California, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, Department of Genome Sciences, University of Washington, Seattle, Washington, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, California | 2 | 2021 | Sina Booeshaghi, Yeokyoung Kil, Kyung Hoi Min, Jase Gehring, Lior Pachter 2021. Assembly Instructions for colosseum. protocols.io https://dx.doi.org/10.17504/protocols.io.btz3np8n | 2021-04-15 09:14:25 | |||
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Mammalian Cell Culture: Refreshing Media Resource Report Resource Website |
Kenneth Schackart, Kattika Kaarj | DOI:10.17504/protocols.io.xqifmue | 481b Laboratory | This protocol explains how to refresh the media of cultured mammalian cells grown in a tissue culture flask. | University of Arizona, University of Arizona | 1 | 2019 | Kenneth Schackart, Kattika Kaarj 2019. Mammalian Cell Culture: Refreshing Media. protocols.io https://dx.doi.org/10.17504/protocols.io.xqifmue | 2021-04-15 09:14:29 | |||
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Protocol for T7 Exonuclease (NEB #M0263) Resource Report Resource Website |
New England Biolabs | New England Biolabs (NEB) | New England Biolabs | https://neb.com/protocols/2019/07/24/protocol-for-t7-exonuclease-m0263 | 1 | 2020 | New England Biolabs 2020. Protocol for T7 Exonuclease (NEB #M0263). protocols.io https:// | 2021-04-15 09:14:25 | ||||
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meta analysis Resource Report Resource Website |
Chuandan Wan | DOI:10.17504/protocols.io.8t4hwqw | A systematic literature search was performed using PubMed, Embase, and WANFANG MED ONLINE databases up to March 18, 2019. All literature was analyzed using Meta Disc 1.4 and STATA 14.0 software. Diagnostic measures of accuracy of ctDNA in cervical cancer were pooled and investigated. Fifteenstudies comprising 1109 patients with cervical cancer met our inclusion criteria and were subjected to analysis. | Gu Y, Wan C, Qiu J, Cui Y, Jiang T, Zhuang Z (2020) Circulating HPV cDNA in the blood as a reliable biomarker for cervical cancer: A meta-analysis. PLoS ONE 15(2): e0224001. doi: 10.1371/journal.pone.0224001 | Laboratory of Molecular biology; Changshu Medical examination institute; Changshu; China | https://www.dovepress.com/diagnostic-value-of-circular-rnas-as-effective-biomarkers-for-cancer-a-peer-reviewed-article-OTT | 1 | 2019 | Chuandan Wan 2019. meta analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.8t4hwqw | 2021-04-15 09:14:31 | ||
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METADAP genetic protocol Resource Report Resource Website |
Eric Deflesselle | DOI:10.17504/protocols.io.ti2ekge | Genomic DNA was extracted from circulating blood leucocytes by using Gentra Puregene Blood Kits according to the manufacturer’s protocol (Qiagen) and was stored at -20°C. The TRKB polymorphismswere genotyped by the IntegraGen company (Evry, France) using the Fluidigm®BioMarkTMHD system (Fluidigm Corporation, CA, USA), using TaqMan allelic discrimination (Coulbault et al., 2006), with the ABI Prism® 7900HT Sequence Detection System (Life Technologies). | Deflesselle E, Colle R, Rigal L, David DJ, Vievard A, Martin S, Becquemont L, Verstuyft C, Corruble E (2018) The TRKB rs2289656 genetic polymorphism is associated with acute suicide attempts in depressed patients: A transversal case control study. PLoS ONE 13(10): e0205648. doi: 10.1371/journal.pone.0205648 | Université Paris Sud (Paris XI) | https://doi.org/10.1371/journal.pone.0205648 | 1 | 2018 | Eric Deflesselle 2018. METADAP genetic protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.ti2ekge | 2021-04-15 09:14:31 | ||
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Peptide fragment (579-601 from HIV-gp41) conjugated to keyhole limpet haemocyanin to be used as HIV immunogen. Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bjibkkan | Chemical synthesis facilitates the generation of peptides which are exceedingly difficult to express in bacteria, peptide/protein backbone modification, the incorporation of unnatural amino acids, and the production or synthesis of D-proteins. The C-terminal cysteine can be added to the amino acidic sequences of HIV peptides (fragment 579-601 of the HIV-gp41 [1]. These peptide fragments were dimerized by cysteine oxidation with dimethyl-sulfoxide [2] to facilitate their conjugation to keyhole limpet hemocyanin that acts as a carrier protein. Reference:McPhee DA, Kemp BE, Cumming S, Stapleton D, Gust ID, Doherty RR. Recognition of envelope and tat protein synthetic peptide analogs by HIV positive sera or plasma. FEBS Lett. 1988;233(2):393-396. doi:10.1016/0014-5793(88)80468-x. Tam JP, Wu CR, Liu w, Zhang JW (1991) Disulfide bond formation in peptides by dimethyl sulfoxide. Scope and applications. J Am Chem Soc 113: 66576662. | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Peptide fragment (579-601 from HIV-gp41) conjugated to keyhole limpet haemocyanin to be used as HIV immunogen.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjibkkan | 2021-04-15 09:14:26 | ||||
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MICRO-DILUCIÓN EN PLACA PARA LA EVALUACIÓN DE LA ACTIVIDAD ANTIMICROBIANA EN 50 uL Resource Report Resource Website |
Germán Alberto Téllez Ramírez, Lily Johanna Toro, Juliana Franco Castrillon, Diana Carolina Henao, Jhon Carlos Castaño Osorio, Grupo De Inmunología Molecular Universidad Del Quindio | DOI:10.17504/protocols.io.8xmhxk6 | Este método es basado en el método clásico de micro-dilución en placa de NCLSS (National Committee of Laboratory Safety and Standards (NCLSS) como fue publicado en Amsterdam, D. 1996. Susceptibility testing of Antimicrobials in liquid media. In 'Antibiotics in Laboratory Medicine', Lorian, V., ed. Fourth Edition, pp.52-111. Williams and Wilkins, Baltimore. Modificado con respecto a la lectura de la placa utilizando un indicador metabólico para incrementar la sensibilidad de la prueba respecto al crecimiento de las bacterias.La realizacion de este protocolo fue posible gracias al apoyo del departamento administrativo de ciencia tecnología e innovacion, Colciencias a traves del proyecto 111356933173 convocatoria569-2012. Este protocolo fue estandarizado con el desarrollo del proyecto de grado "OPTIMIZACIÓN DE UN MÉTODO PARA EVALUAR LA ACTIVIDAD ANTIBACTERIANA IN VITRO EN MICROVOLÚMENES" de la estudiante Juliana Franco para optar por el titulo de Biologa. | Centro de Investigaciones Biomédicas, Centro de Investigaciones Biomédicas - Universidad del Quindío, Centro de Investigaciones Biomédicas - Universidad del Quindío - Colombia, Centro de Investigaciones Biomédicas, Centro de Investigaciones Biomédicas - Universidad del Quindío - Colombia, Centro de Investigaciones Biomédicas - Universidad del Quindío - Colombia | 3 | 2020 | Germán Alberto Téllez Ramírez, Lily Johanna Toro, Juliana Franco Castrillon, Diana Carolina Henao, Jhon Carlos Castaño Osorio, Grupo De Inmunología Molecular Universidad Del Quindio 2020. MICRO-DILUCIÓN EN PLACA PARA LA EVALUACIÓN DE LA ACTIVIDAD ANTIMICROBIANA EN 50 uL . protocols.io https://dx.doi.org/10.17504/protocols.io.8xmhxk6 | 2021-04-15 09:14:28 | ||||
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DNA extraction of Nephila clavipes using the Wizard Genomic DNA Purification kit (Promega) Resource Report Resource Website |
Luiz Filipe Bartoleti, Luiz Filipe Bartoleti | DOI:10.17504/protocols.io.kbhcsj6 | Protocol used to extract whole genome DNA from Nephila clavipes (Araneae: Araneidae) specimens. | University of Campinas, University of Campinas | 1 | 2017 | Luiz Filipe Bartoleti, Luiz Filipe Bartoleti 2017. DNA extraction of Nephila clavipes using the Wizard Genomic DNA Purification kit (Promega) . protocols.io https://dx.doi.org/10.17504/protocols.io.kbhcsj6 | 2021-04-15 09:14:26 | ||||
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1. Flowchart illustrating the steps of the clinical reasoning process Resource Report Resource Website |
Rob A B Oostendorp | DOI:10.17504/protocols.io.uscewaw | 1. Scientific Institute for Quality of Healthcare, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands | 4 | 2018 | Rob A B Oostendorp 2018. 1. Flowchart illustrating the steps of the clinical reasoning process. protocols.io https://dx.doi.org/10.17504/protocols.io.uscewaw | 2021-04-15 09:14:28 | |||||
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Daughter of Frankenstein protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® continuous gradient Resource Report Resource Website |
Luciano Martelotto | DOI:10.17504/protocols.io.bs99nh96 | Human Cell Atlas Method Development Community, Single Cell Core, Harvard Medical School | This protocol is the result of the combination of various nuclei isolation protocols for single cell RNA-seq experiments using droplet-based methods, and is an extension of the Frankenstein (D.O.F means Daughter Of Frankenstein). Developed to prepare nuclei isolates from fresh and frozen material of small-to-large sizes. The good thing is that it does not uses FACS but OptiPrep® continuous gradient to remove debris. It is the alternative protocol when FACS is not available. This protocol works better with smaller samples. After centrifugation the nuclei will form a pellet and contaminating membranes will float at the top. This continuous gradient can be applied for as many times as needed to the same prep to continue cleaning up your nuclei suspensions. | Harvard Medical School | https://singlecellcore.hms.harvard.edu/ | 2 | 2021 | Luciano Martelotto 2021. Daughter of Frankenstein protocol for nuclei isolation from fresh and frozen tissues using OptiPrep® continuous gradient. protocols.io https://dx.doi.org/10.17504/protocols.io.bs99nh96 | 2021-04-15 09:14:26 | ||
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Dye-terminator DNA sequencing Resource Report Resource Website |
Diep Ganguly | DOI:10.17504/protocols.io.bhxmj7k6 | Pogson Genomics Group | This protocol (based on the BigDye® Terminator v3.1 Cycle Sequencing Kit) is for performing terminator cycling sequencing reactions for Sanger sequencing of amplified PCR products or plasmid DNA on the 3130X genetic analyser (Applied Biosystems). | The Australian National University | 5 | 2020 | Diep Ganguly 2020. Dye-terminator DNA sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.bhxmj7k6 | 2021-04-15 09:14:26 | |||
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Observational, Real World Study of Osimertinib for Patients with Locally advanced/Metastatic T790M Mutation-Positive An observational, retrospective study conducted among locally advanced or metastatic T790M mutation-positive NSCLC patients progressed afte Resource Report Resource Website |
Yabing Cao | DOI:10.17504/protocols.io.2qygdxw | EGFR tyrosine kinase inhibitor (TKI) can significantly improve objective response rate (ORR) and prolong progression free survival (PFS) in EGFR mutated locally advanced or metastatic NSCLC patients compared to platinum-based chemotherapy, with less adverse events and higher quality of life (QoL).Osimertinib is an oral, potent, irreversible third-generation EGFR TKI that is selective for EGFR TKI sensitizing mutation and the T790M resistance mutation. Two phase 2 studies(AURA extension, AURA2)have demonstrated encouraging efficacy and tolerable toxicity.However, local data reflecting testing status including testing platform, sample tested, and turnaround time in China is still lacking. The current study will not only assess the effectiveness of osimertinib treatment in a real world setting, but will also help us to understand the real-world testing patterns among T790M mutation positive locally advanced or metastatic NSCLC patients who have progressed after EGFR TKI treatment.Objectives and Hypotheses:The objective of this study is to assess osimertinib effectiveness among locally advanced or metastatic T790M mutation positive NSCLC patients who have progressed after EGFR TKI therapy.The specific study objectives that will be assessed include the following:Primary Objective§ To assess the real world effectiveness of osimertinib treatment in locally advanced or metastatic NSCLC patients with a EGFR T790M mutation in terms of response rate (RR)Secondary Objectives§ To assess the real world effectiveness of osimertinib treatment in locally advanced or metastatic NSCLC patients with a EGFR T790M mutation in terms of progression free survival (PFS)§ To describe the pattern of T790M mutation testing, including turnaround time, sample type, testing techniques, EGFR subtype, T790M mutation abundance if tested quantitatively.§ To assess the real world safety profile of osimertinib§ To describe the treatment pattern including treatment lines and combination therapy (radiotherapy, surgery, etc.) in a real world setting | Cao Y, Qiu X, Xiao G, Hu H, Lin T (2019) Effectiveness and safety of osimertinib in patients with metastatic EGFR T790M-positive NSCLC: An observational real-world study. PLoS ONE 14(8): e0221575. doi: 10.1371/journal.pone.0221575 | kiang wu hospital, Macau | https://doi.org/10.1371/journal.pone.0221575 | 1 | 2019 | Yabing Cao 2019. Observational, Real World Study of Osimertinib for Patients with Locally advanced/Metastatic T790M Mutation-Positive An observational, retrospective study conducted among locally advanced or metastatic T790M mutation-positive NSCLC patients progressed afte. protocols.io https://dx.doi.org/10.17504/protocols.io.2qygdxw | 2021-04-15 09:14:33 |
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