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Authors: Marc Halushka
Group: Human Cell Atlas Method Development Community
Summary: This method describes harvesting of human heart tissues for spatial transcriptomics.
Proper citation: Marc Halushka 2021. Human heart tissue harvesting. protocols.io dx.doi.org/10.17504/protocols.io.brsvm6e6 Copy
Authors: Kei Suzuki, Shinji Kusunoki, Takuma Sadamori, Yuko Tanabe, Junji Itai, Nobuaki Shime
Summary: The objective of this protocol was to compare the Airway ScopeTM(AWS) and the Macintosh laryngoscope (ML) for their performance in tracheal intubations (TIs) performed by emergency medical technicians (EMTs) using mannequin models with liquids in the airway. Rice gruel and mock blood were used to fill the upper airways of mannequins to create mock vomit and hematemesis models, respectively. TIs were performed by certified EMTs after visualizing the glottis using an AWS with an 18-Fr suction catheter and a ML with an 18-Fr suction catheter. TIs with AWS and ML were performed in random order in a comparative crossover trial. The TI success rate was evaluated based on the following: (a) the time taken from laryngoscope insertion into the oral cavity to glottis visualization, tracheal tube passage through the glottis, until the initiation of ventilation and (b) the subjective level of difficulty, which was assessed using a visual analog scale (VAS).
Proper citation: Kei Suzuki, Shinji Kusunoki, Takuma Sadamori, Yuko Tanabe, Junji Itai, Nobuaki Shime 2019. The protocol for the mannequin crossover trial entitled "Comparison of video and conventional laryngoscopes for simulated difficult emergency tracheal intubations in presence of liquids in the airway". protocols.io dx.doi.org/10.17504/protocols.io.3m2gk8e Copy
Authors: James Fallon, Sophie Payne, Janet Keast, Peregrine Osborne
Group: SPARC
Summary: A pelvic nerve array is custom designed for implantation onto the pelvic nerve of male rats. This device is used for long-term (recovery) experiments. The device can electrically stimulate the pelvic nerve as well as record electrically evoked or spontaneous neural activity. Previously, we have successfully implanted rats for 2 months with no reports of biological adverse complications or damage sustained to the array. The surgical procedure is performed under anesthesia and should incorporate all local requirements for standards of animal experimentation, including methods of anesthesia, surgical environment, and post-operative monitoring and care.
Proper citation: James Fallon, Sophie Payne, Janet Keast, Peregrine Osborne 2020. Implantation of a pelvic nerve array in rats. protocols.io dx.doi.org/10.17504/protocols.io.bjvxkn7n Copy
Authors: Shaina Robbins, Sean Nieves
Group: SPARC
Proper citation: Shaina Robbins, Sean Nieves 2020. Staining/Dehydration 10 micron Rat Heart . protocols.io dx.doi.org/10.17504/protocols.io.webfban Copy
Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This protocol describes the delivery of a neuronal tracer using the iontophoretic method. The surgery uses a stereotaxic system to target specific brain coordinates in the mouse. 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. Stereotaxic Surgery for Delivery of Tracers by Iontophoresis. protocols.io dx.doi.org/10.17504/protocols.io.besgjebw Copy
Authors: Ian Mackay, Judy Northill
Group: protocols.io Ambassadors, Public Health Virology, Forensic and Scientific Services
Summary: This test is a modification to the World Health Organization's influenza A H3 TaqMan documented in 'WHO information for molecular diagnosis of influenza virus - update 1' (see file below). New primers were added and the WHO primers discarded.The test targets the hemagglutinin (HA) gene.
Proper citation: Ian Mackay, Judy Northill 2019. Influenza A H3 virus TaqMan assay. protocols.io dx.doi.org/10.17504/protocols.io.74yhqxw Copy
Authors: Somasundhari Shanmuganandam, Benjamin Schwessinger, Robyn Hall
Group: Team Schwessinger
Summary: This is an optimised protocol for 16S library preparation of V3-V4 region for sequencing through Illumina MiSeq platform (2 x 300 bp V3 chemistry). This protocol uses Platinum™ SuperFi™ PCR Master Mix instead of 2x KAPA HiFi HotStart ReadyMix given in Illumina 16S protocol. This polymerase master mix has lower error rate than KAPA, making it more suitable for sequencing.
Proper citation: Somasundhari Shanmuganandam, Benjamin Schwessinger, Robyn Hall 2019. Library preparation protocol to sequence V3-V4 region of 16S rRNA to run in Illumina MiSeq platform. protocols.io dx.doi.org/10.17504/protocols.io.6i7hchn Copy
Authors: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, Patrick Wincker
Group: Tara Oceans
Summary: This protocol describes the 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding for the Tara Oceans expedition and is part of Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition. Figure 1: Overview of -omics analysis strategy applied on Tara Oceans samples.
Proper citation: Adriana Alberti, Julie Poulain, Stefan Engelen, Karine Labadie, Sarah Romac, Isabel Ferrera, Guillaume Albini, Jean-Marc Aury, Caroline Belser, Alexis Bertrand, Corinne Cruaud, Corinne Da Silva, Carole Dossat, Frédéric Gavory, Shahinaz Gas, Julie Guy, Maud Haquelle, E'krame Jacoby, Olivier Jaillon, Arnaud Lemainque, Eric Pelletier, Gaëlle Samson, Marc Wessner, Genoscope Technical Team, Silvia G. Acinas, Marta Royo-Llonch, Francisco M. Cornejo-Castillo, Ramiro Logares, Beatriz Fernández-Gómez, Chris Bowler, Guy Cochrane, Clara Amid, Petra Ten Hoopen, Colomban De Vargas, Nigel Grimsley, Elodie Desgranges, Stefanie Kandels-Lewis, Hiroyuki Ogata, Nicole Poulton, Michael E. Sieracki, Ramunas Stepanauskas, Matthew B. Sullivan, Jennifer R. Brum, Melissa B. Duhaime, Bonnie T. Poulos, Bonnie L. Hurwitz, Stéphane Pesant, Eric Karsenti, Patrick Wincker 2020. 18S and 16S rRNA genes amplicon generation for eukaryotic and prokaryotic metabarcoding. protocols.io dx.doi.org/10.17504/protocols.io.qwhdxb6 Copy
Authors: Matus Valach
Summary: Adapted from the protocol for oligonucleotide 5′ adenylation (E2610) of New England Biolabs (NEB).
Proper citation: Matus Valach 2019. Preparation of the adenylated oligonucleotide for mapping 3′OH RNA termini. protocols.io dx.doi.org/10.17504/protocols.io.xspfndn Copy
Authors: Ian Mackay, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: This protocol was designed and developed at this laboratory.The assay targets the capsid peptide coding region of DENV 1-4 and is desigend as a qualitative screening test for human cases of DENV infection.
Proper citation: Ian Mackay, Judy Northill 2018. Dengue virus (DENV) universal MGB TaqMan 2017. protocols.io dx.doi.org/10.17504/protocols.io.ny8dfzw Copy
Authors: April Woods
Summary: Notes from HAB OOS meeting, April 4 2018, SCCRWP.
Proper citation: April Woods 2018. meeting notes 4/4/2018. protocols.io dx.doi.org/10.17504/protocols.io.n9pdh5n Copy
Authors: LI-COR Biosciences
Group: LI-COR Biosciences
Summary: This protocol describes a method to determine optimal blocking conditions for NIR Western blot detection with the Odyssey family of Imagers.
It is for use with the Odyssey Nitrocellulose membranes or any other commercially-available nitrocellulose membranes.
Proper citation: LI-COR Biosciences 2017. Odyssey Western Blot Blocker Optimization for Near-Infrared (NIR) Detection (nitrocellulose membrane). protocols.io dx.doi.org/10.17504/protocols.io.g7pbzmn Copy
Authors: You Li, Jiri Hulcr
Group: Protocols Bark Beetle Mycobiome
Summary: This protocol describes how to store fungi in slants.This protocol is part of the Bark Beetle Mycobiome (BBM) Research Coordination Network. For more information on the BBM international network: Hulcr J, Barnes I, De Beer ZW, Duong TA, Gazis R, Johnson AJ, Jusino MA, Kasson MT, Li Y, Lynch S, Mayers C, Musvuugwa T, Roets F, Seltmann KC, Six D, Vanderpool D, & Villari C. 2020. Bark beetle mycobiome: collaboratively defined research priorities on a widespread insect-fungus symbiosis. Symbiosis 81: 101–113 https://doi.org/10.1007/s13199-020-00686-9.
Proper citation: You Li, Jiri Hulcr 2020. Mini culture slants for long term storage of fungi. protocols.io dx.doi.org/10.17504/protocols.io.bnu3meyn Copy
Authors: Julie Huber, Caroline Fortunato
Group: Center for Dark Energy Biosphere Investigations, Huber Lab
Summary: This is a RNA extraction protocol adapted from Byron Crump's lab, which was developed from both Zhou et al. 1996 and Crump et al. 2003. It is intended to be used with 47 mm 0.22 um PES filters or a 0.22 uM Sterivex filter, both preserved with RNALater after sample collection.
Proper citation: Julie Huber, Caroline Fortunato 2017. RNA Extraction from Filtered Vent/Crustal Fluids or Seawater. protocols.io dx.doi.org/10.17504/protocols.io.iuxcexn Copy
Authors: Diego Lai
Group: Coronavirus Method Development Community, XPRIZE Rapid Covid Testing
Summary: LooK SPOT COVID-19 antigen rapid test is a lateral flow immunoassay intended for the qualitative detection of nucleocapsid protein antigen from SARS-CoV-2 in nasal swabs from patients suspected of COVID-19 within the first seven (7) days of symptom onset. Testing is limited to laboratories certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA), 42 U.S.C. §263a, that meet the requirements to perform moderate complexity tests. This test is authorized for use at the Point of Care (POC), i.e., in a patient care settings operating under a CLIA Certificate of Waiver, Certificate of Compliance, or Certificate of Accreditation.].Results are for the identification of SARS-CoV-2 nucleocapsid protein antigen. The antigen is generally detectable in nasal samples during the acute phase of infection. Positive results indicate the presence of viral antigens, but the clinical correlation with patient history and other diagnostic information is necessary to determine infection status. Positive results do not rule out a bacterial infection or co-infection with other viruses. The agent detected may not be the definite cause of thedisease. Laboratories within the United States and its territories are required to report all positive results to the appropriate public health authorities.Negative results should be treated as presumptive, and do not rule out SARS-CoV-2 infection, and should not be used as the sole basis for treatment or patient management decisions, including infection control decisions. Negative results should be considered in the context of a patient's recent exposures, history, and the presence of clinical signs and symptoms consistent with COVID-19, and confirmed with a molecular assay, if necessary, for patient management. LooK SPOT COVID-19 Antigen Rapid Test can deliver a diagnosis of the SARS-CoV-2 virus detection between 5 to 8 minutes by using machine learning AI. LooK SPOT’s AI algorithm has high accuracy and can identify the fluorescence response when human eyes cannot identify the low positive cases. Healthcare responders in the COVID-19 test sites often need to make time-sensitive decisions to determine the test results during the time many patients are within their vicinity. But the tempo, volume, stress, fatigue, lighting, fear, and various other factors can overwhelm healthcare responders when making the visual interpretation of antigen test results. It is of paramount importance to reduce healthcare responders' cognitive load by providing accurate test results in an easy-to-read format. LooK SPOT COVID-19 Antigen Rapid Test is a COVID-19 rapid test solution designed with a tactical edge to fight COVID-19. The LooK SPOT COVID-19 Antigen Rapid Test is intended for use at the Point of Care (POC) settings by trained personnel specifically instructed and trained in vitro diagnostic procedures. It is only for use under the Food and Drug Administration's Emergency Use Authorization.
Proper citation: Diego Lai 2020. LooK SPOT Antigen Rapid Test System. protocols.io dx.doi.org/10.17504/protocols.io.bp32mqqe Copy
Authors: Lenny Teytelman
Group: HCA Working Group for SOPs and Sample Metadata
Summary: This is just a draft. Please feel free to revise and comment, but try to keep the total fields to a maximum of 20.
Proper citation: Lenny Teytelman 2019. Minimal sample metadata for healthy liver tissue. protocols.io dx.doi.org/10.17504/protocols.io.8t6hwre Copy
Authors: Judy Northill, Ian Mackay
Summary: NOT RECOMMENDEDThe sensitivity of the assay has been found to be lower than expected and we no longer recommend it be used.We do recommend the ORF1ab assay (Novel coronavirus (2019-nCoV) real-time RT-PCR ORF1ab 2020) or the E gene assay by Corman et al. (Protocol v2-1)A real-time RT-PCR to designed to detect the "novel Wuhan" betacoronavirus. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region encodes the nucleocapsid (N).Not tested on wild-type virus (as of 25Jan2020), it is expected to be capable of detecting Wuhan virus, bat-like SARS and SARS virus.Limit of detection not yet determined.A single 1 mismatch at probe-binding site identified with the BetaCoV/USA/CA1/2020|EPI_ISL_406034 variant of 2019-nCoV (as of 29JAN2020).Probe is in the 3'-5' (reverse complement) direction.A real-time RT-PCR to designed to detect the "novel Wuhan" betacoronavirus. Based on sequence MN908947 made available by Professor Yong-Zhen Zhang, Fudan University, Shanghai, China. The target region encodes the nucleocapsid (N).Not tested on wild-type virus (as of 25Jan2020), it is expected to be capable of detecting Wuhan virus, bat-like SARS and SARS virus.Limit of detection not yet determined.A single 1 mismatch at probe-binding site identified with the BetaCoV/USA/CA1/2020|EPI_ISL_406034 variant of 2019-nCoV (as of 29JAN2020).Probe is in the 3'-5' (reverse complement) direction.Notes: Assay is optimised (as of 24Jan2020).A final name for this virus has not been decided (as of 25Jan2020).
Proper citation: Judy Northill, Ian Mackay 2020. Novel coronavirus (2019-nCoV) real-time RT-PCR N gene 2020 (Wuhan-N; 2019-nCoV-related test) -NOT RECOMMENDED. protocols.io dx.doi.org/10.17504/protocols.io.bb5piq5n Copy
Authors: SARAH SIU TZE MAK, SHYAM GOPALAKRISHNAN, CHRISTIAN CAROE, CHUNYU GENG, SHANLIN LIU, MIKKEL-HOLGER S SINDING, LUKAS F K KUDERNA, WENWEI ZHANG, SHUJIN FU, FILIPE G VIEIRA, MIETJE GERMONPRÉ, HERVÉ BOCHERENS, SERGEY FEDOROV, BENT PETERSEN, THOMAS SICHERITZ-PONTEN, TOMAS MARQUES-BONET, GUOJIE ZHANG, HUI JIANG, M THOMAS P GILBERT
Group: GigaScience Press
Summary: This single-tube library construction protocol is for degraded DNA using BGISeq-500 sequencing platform.
Proper citation: SARAH SIU TZE MAK, SHYAM GOPALAKRISHNAN, CHRISTIAN CAROE, CHUNYU GENG, SHANLIN LIU, MIKKEL-HOLGER S SINDING, LUKAS F K KUDERNA, WENWEI ZHANG, SHUJIN FU, FILIPE G VIEIRA, MIETJE GERMONPRÉ, HERVÉ BOCHERENS, SERGEY FEDOROV, BENT PETERSEN, THOMAS SICHERITZ-PONTEN, TOMAS MARQUES-BONET, GUOJIE ZHANG, HUI JIANG, M THOMAS P GILBERT 2017. BGISeq-500 library construction Protocol. protocols.io dx.doi.org/10.17504/protocols.io.iamcac6 Copy
Authors: Glennis Logsdon
Group: High molecular weight DNA extraction from all kingdoms
Summary: This protocol describes the purification of high-molecular-weight genomic DNA from mammalian cells and the generation of ultra-long (N50 >100 kbp) Oxford Nanopore data. It is based on the Sambrook and Russell protocol and Josh Quick's protocol with additional modifications. This protocol improves upon previous protocols developed for ultra-long read sequencing, as it gives longer reads with greater yield. In our hands, we obtain about 1-2 Gb of ultra-long-read ONT data with an N50 ~150 kbp on one MinION flow cell.
Proper citation: Glennis Logsdon 2020. HMW gDNA purification and ONT ultra-long-read data generation. protocols.io dx.doi.org/10.17504/protocols.io.bchhit36 Copy
Authors: Sophie Martin
Group: EDYCO
Summary: This protocol is intended to help you use HOBO data loggers and HOBOware software.
Proper citation: Sophie Martin 2018. HOBO data loggers. protocols.io dx.doi.org/10.17504/protocols.io.vbye2pw Copy
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