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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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During data acquisition Resource Report Resource Website |
Lukas Snoek, Tinka Beemsterboer | 10.17504/protocols.io.tfrejm6 | 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 | 8 | 2018 | Lukas Snoek, Tinka Beemsterboer 2018. During data acquisition. protocols.io dx.doi.org/10.17504/protocols.io.tfrejm6 | 2021-03-29 03:08:42 | |||
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Food preference assay of C Elegans Resource Report Resource Website |
Priota Islam | 10.17504/protocols.io.yb5fsq6 | Behavioural Genomics | Imperial College London | 1 | 2019 | Priota Islam 2019. Food preference assay of C Elegans. protocols.io dx.doi.org/10.17504/protocols.io.yb5fsq6 | 2021-03-29 03:08:39 | ||||
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ClampFISH Resource Report Resource Website |
Sara H Rouhanifard, Ian A Mellis, Margaret Dunagin, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj | 10.17504/protocols.io.qeydtfw | Human Cell Atlas Method Development Community | Non-enzymatic, high-gain signal amplification methods with single-cell, single-molecule resolution are in great need. We present click-amplifying FISH (clampFISH) for the fluorescent detection of RNA that combines the specificity of oligonucleotides with bioorthogonal click chemistry in order to achieve high specificity and extremely high-gain (>400x) signal amplification. We show that clampFISH signal enables detection with low magnification microscopy and separation of cells by RNA levels via flow cytometry. Additionally, we show that the modular design of clampFISH probes enables multiplexing, that the locking mechanism prevents probe detachment in expansion microscopy, and that clampFISH works in tissue samples. | University of Pennsylvania, University of Pennsylvania, University of Pennsylvania, University of Pennsylvania, University of Pennsylvania, University of Pennsylvania, University of Pennsylvania | https://www.biorxiv.org/content/early/2018/05/07/222794 | 1 | 2018 | Sara H Rouhanifard, Ian A Mellis, Margaret Dunagin, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj 2018. ClampFISH . protocols.io dx.doi.org/10.17504/protocols.io.qeydtfw | 2021-03-29 03:08:40 | ||
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Using a Peristaltic Pump to Flow Buffer Through a Nanoporous Membrane in Filter Holder Assembly Resource Report Resource Website |
Harley King | 10.17504/protocols.io.rwqd7dw | This protocol provides steps for seating and flowing liquid through a 50 μm, 13mm round membrane containing a hexagonal arrangement of 25nm pores with lattice constant 65nm using a peristaltic pump. Porous, alumina membranes are fragile and pressure is required to pass buffer through the 25nm pores.A peristaltic pump at a low flow rate reproducibly hydrates membranes compared to syringe-based assemblies. Steps in this protocol minimize membrane breaks and damage during membrane placement in the filter adapter assembly, liquid flow through the membrane and membrane retrieval. | LuminUltra | 1 | 2020 | Harley King 2020. Using a Peristaltic Pump to Flow Buffer Through a Nanoporous Membrane in Filter Holder Assembly. protocols.io dx.doi.org/10.17504/protocols.io.rwqd7dw | 2021-03-29 03:08:39 | ||||
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Agarose Gel Electrophoresis-Chem 584 Resource Report Resource Website |
Ken Christensen, Addgene The Nonprofit Plasmid Repository | 10.17504/protocols.io.bjvnkn5e | This protocol is for agarose gel electrophoresis. To see the full abstract and additional resources, visit the Addgene protocol page. | Brigham Young University, Addgene | https://www.addgene.org/protocols/gel-electrophoresis/ | 1 | 2020 | Ken Christensen, Addgene The Nonprofit Plasmid Repository 2020. Agarose Gel Electrophoresis-Chem 584 . protocols.io dx.doi.org/10.17504/protocols.io.bjvnkn5e | 2021-03-29 03:08:42 | |||
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Coating of plates with Geltrex, for human iPSC culture Resource Report Resource Website |
Ralitsa Madsen | 10.17504/protocols.io.utcewiw | University of Edinburgh | 1 | 2018 | Ralitsa Madsen 2018. Coating of plates with Geltrex, for human iPSC culture. protocols.io dx.doi.org/10.17504/protocols.io.utcewiw | 2021-03-29 03:08:39 | |||||
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Hybridization-capture for nanopore sequencing Resource Report Resource Website |
Isac Lee, Rachael Workman, Josh Zhiyong Wang, Winston Timp | 10.17504/protocols.io.zxyf7pw | TimpLab | Large-scale genomic anomalies – structural variations (SVs) – are pervasive in cancer. Due to the scale of the SVs and the repetitive nature of the sequences usually flanking them, they are difficult to measure with conventional short-read sequencing. The long reads possible with nanopore sequencing provide an alternative to advance the understanding of SVs. In this application note, we applied SureSelectXT to nanopore long read sequencing, enriching for CDKN2A and SMAD4 tumor suppressor genes, to improve the depth and variant calling accuracy of nanopore sequencing.This application note focuses on optimizing the SureSelectXT protocol to long-read sequencing and using open-source softwares nanopolish and sniffles to improve the base calling accuracy and detect single nucleotide variants (SNVs) and structural variants (SVs), demonstrating the utility of SureSelect system on third-generation long-read sequencing platforms. | Johns Hopkins University, Johns Hopkins University, Agilent Technologies, Johns Hopkins University | 1 | 2019 | Isac Lee, Rachael Workman, Josh Zhiyong Wang, Winston Timp 2019. Hybridization-capture for nanopore sequencing. protocols.io dx.doi.org/10.17504/protocols.io.zxyf7pw | 2021-03-29 03:08:42 | |||
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Fixation of Planktonic Samples Resource Report Resource Website |
Matthew Sullivan | 10.17504/protocols.io.c3ayid | VERVE Net, Sullivan Lab | Modified after Glöckner et al. 1999 | Matthe Sullivan Lab, University of Arizona/Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Fixation of Planktonic Samples. protocols.io dx.doi.org/10.17504/protocols.io.c3ayid | 2021-03-29 03:08:42 | |||
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Artificial Cerebrospinal Fluid III (ACSF.III) Resource Report Resource Website |
Allen Institute for Brain Science | 10.17504/protocols.io.bdpci5iw | BICCN, Allen Institute for Brain Science | Artificial Cerebrospinal Fluid III (ACSF.III) is used for applications including tissue bath solution during electrophysiological recording.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 2 | 2020 | Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid III (ACSF.III). protocols.io dx.doi.org/10.17504/protocols.io.bdpci5iw | 2021-03-29 03:08:39 | |||
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ELISA for quantification of macrophage-colony stimulating factor (M-CSF) in human serum or plasma. Resource Report Resource Website |
Angel Justiz-Vaillant | 10.17504/protocols.io.bksskwee | Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. [1]The immunoregulatory cytokine IL-41 (also known as meteorin-like protein) is expressed at high levels in the synovium of patients with psoriatic arthritis (PsA).[2]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019.2.Onuora S. Novel cytokine, IL-41, linked with PsA.Nat Rev Rheumatol. 2019;15(11):636. doi:10.1038/s41584-019-0314-7 | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. ELISA for quantification of macrophage-colony stimulating factor (M-CSF) in human serum or plasma.. protocols.io dx.doi.org/10.17504/protocols.io.bksskwee | 2021-03-29 03:08:41 | ||||
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Isolation of Salmonella pathogens from oysters Resource Report Resource Website |
Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant | 10.17504/protocols.io.bj6qkrdw | University of the West Indies, [email protected] | University of the West Indies St. Augustine, University of the West Indies St. Augustine, University of the West Indies St. Augustine, University of the West Indies St. Augustine, University of the West Indies. St. Augustine | 1 | 2020 | Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant 2020. Isolation of Salmonella pathogens from oysters. protocols.io dx.doi.org/10.17504/protocols.io.bj6qkrdw | 2021-03-29 03:08:39 | ||||
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Cell DIVE™ Platform | Antibody Purification Chemistry Resource Report Resource Website |
Anup Sood, Eric Williams, Liz McDonough | 10.17504/protocols.io.bpx9mpr6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research | The purpose of the protocol is to purify antibodies that will be conjugated to Cy dyes as per the Cell DIVE™ technology. Affinity chromatography will be used to remove impurities from the vendor antibody to enable conjugation. | GE Research, GE Research, GE Research | 1 | 2021 | Anup Sood, Eric Williams, Liz McDonough 2021. Cell DIVE™ Platform | Antibody Purification Chemistry. protocols.io dx.doi.org/10.17504/protocols.io.bpx9mpr6 | 2021-03-29 03:08:40 | |||
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Preparation of the sgRNA-Barcode Amplicon Library Resource Report Resource Website |
Shiqi Xie, Anne Cooley, Gary Hon | 10.17504/protocols.io.pufdntn | Xie S, Cooley A, Armendariz D, Zhou P, Hon GC (2018) Frequent sgRNA-barcode recombination in single-cell perturbation assays. PLoS ONE 13(6): e0198635. doi: 10.1371/journal.pone.0198635 | Green Center for Reproductive Biology, Department of Obestetrics and Gynecology, UT Southwestern Medical Center, Green Center for Reproductive Biology, Department of Obestetrics and Gynecology, UT Southwestern Medical Center, Green Center for Reproductive Biology, Department of Obestetrics and Gynecology, UT Southwestern Medical Center | https://doi.org/10.1371/journal.pone.0198635 | 1 | 2018 | Shiqi Xie, Anne Cooley, Gary Hon 2018. Preparation of the sgRNA-Barcode Amplicon Library. protocols.io dx.doi.org/10.17504/protocols.io.pufdntn | 2021-03-29 03:08:41 | |||
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Optimized protocol for brain and head kidney catalase activity in zebrafish Resource Report Resource Website |
Caio Maximino, Bruna Patrícia Dutra Costa, Gabriel Rocha Felício | 10.17504/protocols.io.rumd6u6 | Fish behavior and physiology | Zebrafish, and other small teleosts, are used as experimental models to evaluate human pathologies, including those linked to oxidative stress. The protocol presents an optimized technique to evaluate the activity of catalase, an important antioxidant enzyme, in zebrafish tissues, focusing on the brain and head kidney. The protocol is based on the classical Aebi (1984) method. | Universidade Federal do Sul e Sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará, Universidade Federal do Sul e Sudeste do Pará | 1 | 2018 | Caio Maximino, Bruna Patrícia Dutra Costa, Gabriel Rocha Felício 2018. Optimized protocol for brain and head kidney catalase activity in zebrafish. protocols.io dx.doi.org/10.17504/protocols.io.rumd6u6 | 2021-03-29 03:08:41 | |||
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Illumina metabarcoding protocol for the study of fungi in marine sediments Resource Report Resource Website |
Lluvia Vargas-Gastélum, Jennyfers Chong-Robles, Asunción Lago-Lestón, Meritxell Riquelme | 10.17504/protocols.io.yupfwvn | Marine Fungi, Riquelme CICESE | The study of fungi in marine sediments has received a growing attention in the recent years. Recent advances in metagenomics have allowed the discovery of a wide diversity of fungi in deep-sea environments, although standardized methods are needed to process the samples and to analyze the data. This protocol is a guidance to obtain good quality samples and subsequent ITS1 (Internal Transcribed Spacer 1) amplicons to be prepared for sequencing by Illumina platform. The collection of marine sediments is described, as well as the processing of the samples in laboratory; also, pertinent controls that should be included during all the processing steps to identify potential sources of contamination that could affect the sequencing and bias the interpretation of results are suggested. | Centro de Investigación y de Educación Superior de Ensenada, CICESE, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE, Centro de Investigación Científica y de Educación Superior de Ensenada, CICESE | 1 | 2019 | Lluvia Vargas-Gastélum, Jennyfers Chong-Robles, Asunción Lago-Lestón, Meritxell Riquelme 2019. Illumina metabarcoding protocol for the study of fungi in marine sediments. protocols.io dx.doi.org/10.17504/protocols.io.yupfwvn | 2021-03-29 03:08:41 | |||
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Extraction and Purification of Anthocyanin from Potato Resource Report Resource Website |
Fang Liu, Yuanjun Yang, Jianwei Gao, Changle Ma, Yuping Bi | 10.17504/protocols.io.ma4c2gw | This is a protocol for extraction and purification of anthocyanin from potato. | Liu F, Yang Y, Gao J, Ma C, Bi Y (2018) A comparative transcriptome analysis of a wild purple potato and its red mutant provides insight into the mechanism of anthocyanin transformation. PLoS ONE 13(1): e0191406. doi: 10.1371/journal.pone.0191406 | College of Life Science, Shandong Normal University, PR China;Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences,PR China, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences,PR China, Institute of Vegetables and Flowers, Shandong Academy of Agricultural Sciences,PR China, College of Life Science, Shandong Normal University, PR China, College of Life Science, Shandong Normal University, PR China;Biotechnology Research Center, Shandong Academy of Agricultural Sciences, PR China | https://doi.org/10.1371/journal.pone.0191406 | 1 | 2018 | Fang Liu, Yuanjun Yang, Jianwei Gao, Changle Ma, Yuping Bi 2018. Extraction and Purification of Anthocyanin from Potato. protocols.io dx.doi.org/10.17504/protocols.io.ma4c2gw | 2021-03-29 03:08:41 | ||
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Human subchondral osteoblasts cell culture Resource Report Resource Website |
Christelle Sanchez | 10.17504/protocols.io.mkmc4u6 | Method of isolation and culture of osteoblast coming from human subchondral bone of the knee | Sanchez C, Mazzucchelli G, Lambert C, Comblain F, DePauw E, Henrotin Y (2018) Comparison of secretome from osteoblasts derived from sclerotic versus non-sclerotic subchondral bone in OA: A pilot study. PLoS ONE 13(3): e0194591. doi: 10.1371/journal.pone.0194591 | Bone and Cartilage Research Unit, University of Liège, Belgium | https://doi.org/10.1371/journal.pone.0194591 | 1 | 2018 | Christelle Sanchez 2018. Human subchondral osteoblasts cell culture. protocols.io dx.doi.org/10.17504/protocols.io.mkmc4u6 | 2021-03-29 03:08:41 | ||
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During Data Acquisition Resource Report Resource Website |
Lukas Snoek | 10.17504/protocols.io.jrbcm2n | Spinoza Centre, REC-L | This is a test | Spinoza Centre, REC-L | 1 | 2017 | Lukas Snoek 2017. During Data Acquisition. protocols.io dx.doi.org/10.17504/protocols.io.jrbcm2n | 2021-03-29 03:08:41 | |||
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Cell Fixation and Permeabilization Protocol using 70% Ethanol Resource Report Resource Website |
Kelsey Miller | 10.17504/protocols.io.hv3b68n | BioLegend | Cell Fixation and Permeabilization Protocol Using 70% Ethanol | BioLegend | http://www.biolegend.com/media_assets/support_protocol/BioLegend_EthFIXPERM_032912.pdf | 2 | 2017 | Kelsey Miller 2017. Cell Fixation and Permeabilization Protocol using 70% Ethanol. protocols.io dx.doi.org/10.17504/protocols.io.hv3b68n | 2021-03-29 03:08:40 | ||
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Longitudinal Analysis of C elegans (L4, YA D2 & YA D5) Resource Report Resource Website |
Priota Islam | 10.17504/protocols.io.bbk2ikye | Behavioural Genomics | Imperial College London | 1 | 2020 | Priota Islam 2020. Longitudinal Analysis of C elegans (L4, YA D2 & YA D5). protocols.io dx.doi.org/10.17504/protocols.io.bbk2ikye | 2021-03-29 03:08:40 |
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