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Authors: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones
Group: RENE FLORES
Summary: DNA extraction and quantification
Proper citation: Rene Flores Clavo, Cristian Daniel Asmat Ortega, Nataly Ruiz Quinones 2021. DNA extraction and quantification . protocols.io dx.doi.org/10.17504/protocols.io.bsj4ncqw Copy
Authors: oomaliwa
Proper citation: oomaliwa 2021. Predictors of Death Less Than versus More Than 90 days after Receiving a Modified Blalock-Taussig Shunt in Cyanotic Heart Children. protocols.io dx.doi.org/10.17504/protocols.io.bqz8mx9w Copy
Authors: Ken Youens-Clark
Group: MetaFunc Course
Summary: Yeast is a well-characterized genome due to its small size and historical significance in genetics. The website http://yeastgenome.org/ is a dedicated resource for yeast genomics.
Proper citation: Ken Youens-Clark 2016. Command line exercises with yeast. protocols.io dx.doi.org/10.17504/protocols.io.fnebmbe Copy
Authors: LI-COR Biosciences
Group: LI-COR Biosciences
Summary: This is a complete apoptosis assay example. It details the seeding, induction, and detection of the HeLa cellular response to Anisomycin treatment.
Developed for:
Aerius,
Odyssey® Classic,
Odyssey CLx, and
Odyssey Sa
Infrared Imaging Systems
Please refer to your manual to confirm that this protocol is appropriate for the applications compatible with your Odyssey Imager model.
Proper citation: LI-COR Biosciences 2018. In-Cell Western™ Assay (HeLa Cellular Response to Anisomycin Treatment). protocols.io dx.doi.org/10.17504/protocols.io.gwibxce Copy
Authors: Nicholas Boudreau
Summary: Purpose of this protocol is to grow up single colonies of bacteria for use.
Proper citation: Nicholas Boudreau 2018. Overnight Bacterial Batch Culture. protocols.io dx.doi.org/10.17504/protocols.io.nv3de8n Copy
Authors: Zehra Kahveci
Group: Pagliara Lab
Summary: Preparation of giant unilamellar vesicels (GUVs) by electroformation method has been detailed. 10 to 100 micrometer size GUVs obtained after the process.
Proper citation: Zehra Kahveci 2018. Giant Unilamellar Vesicles (GUVs) Preparation by Electroformation Method. protocols.io dx.doi.org/10.17504/protocols.io.rvvd666 Copy
Authors: BinnypreetKaur1, 2, DrahomíraFaktorová1, 2, PriscilaPeñaDiaz1andJuliusLukeš1, 2
Group: Julius Lukes
Proper citation: BinnypreetKaur1, 2, DrahomíraFaktorová1, 2, PriscilaPeñaDiaz1andJuliusLukeš1, 2 2018. Alamar Blue Assay: Drug Sensitivity Test. protocols.io dx.doi.org/10.17504/protocols.io.hhfb33n Copy
Authors: Eliana Rocio Rodríguez Gómez, William Otero Regino, Pedro A. Monterrey, Alba Alicia Trespalacios Rangel
Summary: In this study , we aimed to determine the current circulation of cagA gene EPIYA motifs present in Colombian Helicobacter pylori isolates using a rapid molecular test. The cagA gene 3' region was amplified through conventional Polymerase Chain Reaction (PCR) and PCR products obtained were sequenced and analyzed with bioinformatics tools.Aditionally, to confirm the prediction of the number EPIYA C repeats based on the PCR product molecular weight, reamplification and secuencing analysis were performed.
Proper citation: Eliana Rocio Rodríguez Gómez, William Otero Regino, Pedro A. Monterrey, Alba Alicia Trespalacios Rangel 2019. Molecular biology test for rapid detection cagAgen EPIYA motif in H.pylori isolates. protocols.io dx.doi.org/10.17504/protocols.io.54jg8un Copy
Authors: Marda Jorgensen, Jerelyn Nick
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This protocol describes the method for antibody staining of FFPE tissues on coverslips using CODEX Barcoded Antibodies. Included are the stepwise protocols for pre-staining, deparaffinization, antigen retrival, antibody staining and post-fixation. The enitre process requires approximately 6.5 hours, including a 3 hour incubation. Except as noted, reagents and consumables should be prepared before being the protocol. Stained tissues can be stored in CODEX Storage Buffer at 4º C for up to 2 weeks for use in CODEX multiplex imaging.
Proper citation: Marda Jorgensen, Jerelyn Nick 2020. CODEX Antibody Staining Protocol for FFPE tissues. protocols.io dx.doi.org/10.17504/protocols.io.bbsdina6 Copy
Authors: Maja Rennig, Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm
Summary: The methylotrophic yeast Komagataella phaffii (formerly Pichia pastoris) is the most commonly used yeast species in the production of recombinant proteins. This is most likely due to its ability to grow to high cell density, to express recombinant genes in a tightly controlled manner and to efficiently secrete proteins. Despite its biotechnological importance and wide use in industry, relatively few genetic tools are readily available for academic research. Here, we present a protocol for production of proteins in K. phaffii.The protocol found here is modified from the protocol provided in the Pichia Expression Kit (Catalog Number K1710-01, Invitrogen).
Proper citation: Maja Rennig, Kristoffer Bach Falkenberg, Cristina Hernandez Rollan, Andreas Birk Bertelsen, Morten Norholm 2020. Protein expression in Komagataella phaffii (formerly Pichia pastoris). protocols.io dx.doi.org/10.17504/protocols.io.bd32i8qe Copy
Authors: Rustam Al-Shahi Salman, Martin S. Dennis, Kasia Adamczuk, Karen Innes, Ruth Fraser, Jonathan Drever, Lynn Dinsmore, Carol Williams, Steff Lewis, Philip M. White, David E. Newby, Gregory Y.H. Lip, Adrian Parry-Jones, Dan Lasserson, Colin Oliver, Joanna Wardlaw, John Norrie
Summary: Primary research questionFor adults surviving spontaneous (non-traumatic) symptomatic intracranial haemorrhage with persistent/paroxysmal atrial fibrillation/flutter (AF), does starting full treatment dose oral anticoagulation (OAC) result in a beneficial net reduction of all serious vascular events compared with not starting OAC?Trial designInvestigator-led, multicentre, randomised, open, assessor-masked, parallel group, clinical trial of investigational medicinal product (CTIMP) prescribing strategies. We plan for a pilot phase, followed by a safety phase.ObjectivesPilot phase: ~30 hospital sites keep screening logs and recruit at least 60 participants >24 hours after spontaneous symptomatic intracranial haemorrhage with AF and a CHA2DS2-VASc score ≥2 to determine the acceptability and feasibility of recruiting the target sample size in a definitive trial in an acceptable timescale.Safety phase: ~60 hospital sites will recruit at least 190 participants to determine whether the risk of recurrent symptomatic intracranial haemorrhage is sufficiently low (non-inferior) to justify a definitive trial.Eligibility criteriaInclusion: Spontaneous symptomatic intracranial haemorrhage, AF and a CHA2DS2-VASc score ≥2.Exclusion: Patient age Brain magnetic resonance imaging (MRI) sub-study: MRI must be done after intracranial haemorrhage but before randomisation. Sub-study participants must not have contraindications to MRI. SettingRecruitment in secondary care (inpatient and outpatient services in stroke, general internal medicine, medicine of the elderly, cardiology, neurology and neurosurgery) with follow-up in primary and secondary care.RandomisationCentral, web-based randomisation, with 1:1 allocation of intervention: comparator, using a minimisation algorithm.InterventionStart long-term (≥1 year) full treatment dose OAC (either a non-vitamin K antagonist direct oral anticoagulant [DOAC] or vitamin K antagonist if a DOAC cannot be used), chosen by the patient’s physician before randomisation.Comparators Do not start OAC (standard clinical practice without OAC may include antiplatelet drug(s) or no antithrombotic drugs).Outcome measuresPilot phase: The proportions of eligible patients who are recruited, unsuitable, or decline to participate; the acceptability of the trial protocol to investigators and patients; and the rate of recruitment per site.Safety phase: Primary outcome: Recurrent, symptomatic, spontaneous intracranial haemorrhage. Exploratory outcomes: All symptomatic serious vascular events (i.e. major adverse cardiac or cerebrovascular events [MACCE]) including non-fatal stroke and spontaneous subdural haemorrhage, non-fatal myocardial infarction, vascular death, sudden death, or death of unknown cause. Individual symptomatic vascular events. Individual types of fatal events. Dependence according to the modified Rankin Scale.Follow upAt least one year after randomisation, using annual questionnaires to participants and their GPs, including review of any medical records and brain imaging relating to outcomes.Sample sizeWe plan to recruit at least 60 participants in a pilot phase and at least 190 participants in a safety phase (12% equivalence margin in the outcome of symptomatic intracranial haemorrhage, 1-sided p=0.025 and power 90%).
Proper citation: Rustam Al-Shahi Salman, Martin S. Dennis, Kasia Adamczuk, Karen Innes, Ruth Fraser, Jonathan Drever, Lynn Dinsmore, Carol Williams, Steff Lewis, Philip M. White, David E. Newby, Gregory Y.H. Lip, Adrian Parry-Jones, Dan Lasserson, Colin Oliver, Joanna Wardlaw, John Norrie 2020. Start or STop Anticoagulants Randomised Trial (SoSTART) after spontaneous intracranial haemorrhage. protocols.io dx.doi.org/10.17504/protocols.io.bcw4ixgw Copy
Authors: Sonia Hall
Proper citation: Sonia Hall 2015. Western Blot - Whole Embryonic Sample. protocols.io dx.doi.org/10.17504/protocols.io.cn2vgd Copy
Authors: Alexandro Rodríguez-Rojas
Group: Alexandro Rodriguez-Rojas
Summary: Preparation of bacterial cell lysate for proteomics (LC-MS) by freeze and thaw cycles
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Proper citation: Alexandro Rodríguez-Rojas 2020. Preparation of bacterial cell lysate for proteomics (LC-MS) by freeze and thaw cycles. protocols.io dx.doi.org/10.17504/protocols.io.bkejktcn Copy
Authors: Julie Haendiges, Narjol Gonzalez-Escalona, Ruth Timme, Maria Balkey
Summary: This procedure outlines the protocol for whole genome sequencing of bacterial organisms using the Illumina DNA Prep library preparation kit for sequencing on an Illumina MiSeq sequencer. 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 (Included SOP 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 (Included SOP or Library Preparation using Illumina Nextera XT )Library preparation using NexteraXT or Illumina DNA Prep (previously Nextera DNA Flex)3. Library Preparation for WGS (Included SOP or Library Preparation using Illumina Nextera XT )4. Sequencing using Illumina MiSeq5. Data Quality Checks and NCBI Submission
Proper citation: Julie Haendiges, Narjol Gonzalez-Escalona, Ruth Timme, Maria Balkey 2020. Illumina DNA Prep (M) Tagmentation Library Preparation for use on an Illumina MiSeq Sequencer. protocols.io dx.doi.org/10.17504/protocols.io.bcbnisme Copy
Authors: Dana M Cataldo, Andrea B Migliano, Lucio Vinicius
Summary: Training of subjects and execution of flintknapping sessions followed a written protocol strictly followed by a skilled tutor. The general protocol is presented as well as its treatment-specific variants.
Proper citation: Dana M Cataldo, Andrea B Migliano, Lucio Vinicius 2018. Speech, stone tool-making and the two-step evolution of language. Experimental protocols.. protocols.io dx.doi.org/10.17504/protocols.io.jyycpxw Copy
Authors: Kelly Cristina Lira de Andrade, Thamyres Ataíde Bezerra Verçosa, Aline Tenório Lins Carnaúba, Pedro de Lemos Menezes
Group: Tecnology and Hearing Laboratory - LATEC
Summary: The present protocol aims to perform the screening of the subjects of the research investigating the auditory normality criteria. Thus, auditory symptoms, health history, medication use, exposure to noise and others are analyzed.
Proper citation: Kelly Cristina Lira de Andrade, Thamyres Ataíde Bezerra Verçosa, Aline Tenório Lins Carnaúba, Pedro de Lemos Menezes 2019. Protocol for evaluation of normal hearing criteria. protocols.io dx.doi.org/10.17504/protocols.io.wsvfee6 Copy
Authors: Stephen Floor
Group: Stephen Floor Lab
Summary: Standard protocol to transform bacteria with a plasmid using chemically competent E. coli and antibiotic resistance.
Proper citation: Stephen Floor 2018. Bacterial transformation. protocols.io dx.doi.org/10.17504/protocols.io.mnwc5fe Copy
Authors: Sean Misek
Group: Neubig_Lab
Proper citation: Sean Misek 2018. Routine Cell Culture. protocols.io dx.doi.org/10.17504/protocols.io.q2jdycn Copy
Authors: Fawaz G. Haj
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary:
This test is designated to determine defects in the insulin signaling pathway, through evaluation of the activation state of the insulin receptor (IR) and its substrate (IRS1/2), as well as downstream target, mainly Akt and MAP kinases.
Proper citation: Fawaz G. Haj 2019. UC Davis - Insulin signaling pathway. protocols.io dx.doi.org/10.17504/protocols.io.yp2fvqe Copy
Authors: Atsuko Mizoguchi
Summary: Total RNA was extracted from cells and the cultured supernatant and exosome which was extracted from the same amount of supernatant using 3D-Gene® RNA extraction reagent.Comprehensive miRNA and mRNA expression analysis were performed using 3D-Gene® Human miRNA Oligo Chip (miRBase ver.21) and mRNA Oligo Chip(Toray Industries, Inc.) which are featured with the columnar structure and bead-mixing for high sensitivity.
Proper citation: Atsuko Mizoguchi 2018. Purification of total RNA (microRNA and mRNA) from liquid samples. protocols.io dx.doi.org/10.17504/protocols.io.vu3e6yn Copy
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