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Authors: Lukas Snoek, Tinka Beemsterboer
Group: Spinoza Centre, REC-L
Summary: 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.
Proper citation: Lukas Snoek, Tinka Beemsterboer 2018. During data acquisition. protocols.io dx.doi.org/10.17504/protocols.io.tfrejm6 Copy
Authors: Priota Islam
Group: Behavioural Genomics
Proper citation: Priota Islam 2019. Food preference assay of C Elegans. protocols.io dx.doi.org/10.17504/protocols.io.yb5fsq6 Copy
Authors: Sara H Rouhanifard, Ian A Mellis, Margaret Dunagin, Sareh Bayatpour, Orsolya Symmons, Allison Cote, Arjun Raj
Group: Human Cell Atlas Method Development Community
Summary: 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.
Proper citation: 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 Copy
Authors: Harley King
Summary: 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.
Proper citation: 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 Copy
Authors: Ken Christensen, Addgene The Nonprofit Plasmid Repository
Summary: This protocol is for agarose gel electrophoresis. To see the full abstract and additional resources, visit the Addgene protocol page.
Proper citation: Ken Christensen, Addgene The Nonprofit Plasmid Repository 2020. Agarose Gel Electrophoresis-Chem 584 . protocols.io dx.doi.org/10.17504/protocols.io.bjvnkn5e Copy
Authors: Ralitsa Madsen
Proper citation: Ralitsa Madsen 2018. Coating of plates with Geltrex, for human iPSC culture. protocols.io dx.doi.org/10.17504/protocols.io.utcewiw Copy
Authors: Isac Lee, Rachael Workman, Josh Zhiyong Wang, Winston Timp
Group: TimpLab
Summary: 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.
Proper citation: 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 Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Modified after Glöckner et al. 1999
Proper citation: Matthew Sullivan 2016. Fixation of Planktonic Samples. protocols.io dx.doi.org/10.17504/protocols.io.c3ayid Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: 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.
Proper citation: Allen Institute for Brain Science 2020. Artificial Cerebrospinal Fluid III (ACSF.III). protocols.io dx.doi.org/10.17504/protocols.io.bdpci5iw Copy
Authors: Angel Justiz-Vaillant
Summary: 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
Proper citation: 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 Copy
Authors: Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Proper citation: 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 Copy
Authors: Anup Sood, Eric Williams, Liz McDonough
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community, GE Research
Summary: 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.
Proper citation: Anup Sood, Eric Williams, Liz McDonough 2021. Cell DIVE™ Platform | Antibody Purification Chemistry. protocols.io dx.doi.org/10.17504/protocols.io.bpx9mpr6 Copy
Authors: Shiqi Xie, Anne Cooley, Gary Hon
Proper citation: Shiqi Xie, Anne Cooley, Gary Hon 2018. Preparation of the sgRNA-Barcode Amplicon Library. protocols.io dx.doi.org/10.17504/protocols.io.pufdntn Copy
Authors: Caio Maximino, Bruna Patrícia Dutra Costa, Gabriel Rocha Felício
Group: Fish behavior and physiology
Summary: 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.
Proper citation: 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 Copy
Authors: Lluvia Vargas-Gastélum, Jennyfers Chong-Robles, Asunción Lago-Lestón, Meritxell Riquelme
Group: Marine Fungi, Riquelme CICESE
Summary: 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.
Proper citation: 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 Copy
Authors: Fang Liu, Yuanjun Yang, Jianwei Gao, Changle Ma, Yuping Bi
Summary: This is a protocol for extraction and purification of anthocyanin from potato.
Proper citation: 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 Copy
Authors: Christelle Sanchez
Summary: Method of isolation and culture of osteoblast coming from human subchondral bone of the knee
Proper citation: Christelle Sanchez 2018. Human subchondral osteoblasts cell culture. protocols.io dx.doi.org/10.17504/protocols.io.mkmc4u6 Copy
Authors: Lukas Snoek
Group: Spinoza Centre, REC-L
Summary: This is a test
Proper citation: Lukas Snoek 2017. During Data Acquisition. protocols.io dx.doi.org/10.17504/protocols.io.jrbcm2n Copy
Authors: Kelsey Miller
Group: BioLegend
Summary: Cell Fixation and Permeabilization Protocol Using 70% Ethanol
Proper citation: Kelsey Miller 2017. Cell Fixation and Permeabilization Protocol using 70% Ethanol. protocols.io dx.doi.org/10.17504/protocols.io.hv3b68n Copy
Authors: Priota Islam
Group: Behavioural Genomics
Proper citation: Priota Islam 2020. Longitudinal Analysis of C elegans (L4, YA D2 & YA D5). protocols.io dx.doi.org/10.17504/protocols.io.bbk2ikye Copy
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