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Aquatic Monitoring Protocol for measuring and collecting ecological data Resource Report Resource Website |
Rebecca Hufft, Margo Paces, Meghan McGill, Richard Levy | DOI:10.17504/protocols.io.9j3h4qn | Denver Botanic Gardens Research and Conservation | This protocol outlines the basic methods for measuring water quality and aquatic macroinvertebrate diversity. These measurements estimate the abundance and presence of aquatic macroinvertebrate species in an area, and link them to environmental conditions (plant community, water temperature and pH, water nutrients, etc.) that may affect their distributions. Together, these data can reveal patterns in aquatic community or ecosystem processes. The stream measurements can be done independently but are usually paired with plant monitoring plots. When a plant monitoring plot is next to a creek or stream, the aquatic sampling occurs in the body of water nearest to the origin of the plant plot. See vegetation monitoring protocol (Hufft et al 2019) for more details. | Denver Botanic Gardens, Denver Botanic Gardens, Denver Botanic Gardens, Denver Botanic Gardens | 1 | 2019 | Rebecca Hufft, Margo Paces, Meghan McGill, Richard Levy 2019. Aquatic Monitoring Protocol for measuring and collecting ecological data. protocols.io https://dx.doi.org/10.17504/protocols.io.9j3h4qn | 2021-04-15 09:14:35 | |||
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Milliplex Cardiovascular Disease 3-plex Panel 2 Resource Report Resource Website |
Ligia Pinto, Troy Kemp | DOI:10.17504/protocols.io.hvcb62w | Luminex Milliplex Cardiovascular Disease 3-plex Panel 2 instructions per manufacturer. | Dyke ALV, Kuhs KAL, Shiels MS, Koshiol J, Trabert B, Loftfield E, Purdue MP, Wentzensen N, Pfeiffer RM, Katki HA, Hildesheim A, Kemp TJ, Pinto LA, Chaturvedi AK, Safaeian M (2017) Associations between self-reported diabetes and 78 circulating markers of inflammation, immunity, and metabolism among adults in the United States. PLoS ONE 12(7): e0182359. doi: 10.1371/journal.pone.0182359 | Human Papilloma Virus Immunology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Human Papilloma Virus Immunology Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research | https://doi.org/10.1371/journal.pone.0182359 | 1 | 2017 | Ligia Pinto, Troy Kemp 2017. Milliplex Cardiovascular Disease 3-plex Panel 2. protocols.io https://dx.doi.org/10.17504/protocols.io.hvcb62w | 2021-04-15 09:14:28 | ||
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Brad-seq mRNA (for Shotgun or DGE) Resource Report Resource Website |
Yin-Tse Huang | DOI:10.17504/protocols.io.bqyymxxw | Kyoto University | 1 | 2020 | Yin-Tse Huang 2020. Brad-seq mRNA (for Shotgun or DGE). protocols.io https://dx.doi.org/10.17504/protocols.io.bqyymxxw | 2021-04-15 09:14:35 | |||||
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NEBExpress Ni Resin Pressurized Column Typical Protocol (NEB #S1428) Resource Report Resource Website |
New England Biolabs | DOI:10.17504/protocols.io.bfa4jigw | New England Biolabs (NEB) | NEBExpress® Ni Resin is an affinity matrix for the isolation and purification of polyhistidine-tagged (His-tagged) fusion proteins. It is intended for use in gravity or pressure flow columns, and batch purifications. NEBExpress Ni Resin is comprised of a highly uniform and stable chemical-tolerant resin, pre-charged with nickel ions on the matrix surface. It is resistant to a wide range of chemicals, including NaOH, EDTA, DTT and β-Mercaptoethanol.Purification of ≥10 mg His-tagged protein per 1 ml of resinIntended for use in gravity or pressure flow columns, and batch purificationsHigh specific binding of His-tagged proteins yielding purities of >95%Strong nickel ion binding provides excellent resistance to EDTA and reducing agents. Compatible with commercially available detergent-based cell lysis reagentsIsolation and purification of His-tagged fusion proteins under native or denaturing conditions | New England Biolabs | https://www.neb.com/protocols/2019/09/10/nebexpress-ni-resin-pressurized-column-protocol-neb-s1428 | 1 | 2020 | New England Biolabs 2020. NEBExpress Ni Resin Pressurized Column Typical Protocol (NEB #S1428). protocols.io https://dx.doi.org/10.17504/protocols.io.bfa4jigw | 2021-04-15 09:14:28 | ||
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1X CviJI Assay Buffer Resource Report Resource Website |
DAVID DUNIGAN AND IRINA AGARKOVA | DOI:10.17504/protocols.io.espbedn | VERVE Net | For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella. | 1 | 2016 | DAVID DUNIGAN AND IRINA AGARKOVA 2016. 1X CviJI Assay Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.espbedn | 2021-04-15 09:14:28 | ||||
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Improving pneumonia diagnoses using pulse oximetry at rural health institutions in southern Ethiopia: Protocol for a cluster-randomized controlled trial Resource Report Resource Website |
Solomon Hailemariam1, 2, 3*, Yabibal Gebeyehu4, Eskinder Loha1, 5, Kjell Arne Johansson2, Bernt Lindtjørn1, 2 | DOI:10.17504/protocols.io.88mhzu6 | Abstract Background: Hypoxemia is common in children with pneumonia. The World Health Organization and United Nations Children’s Fund developed the Integrated Management of Childhood Illness strategy for diagnosing pneumonia. But the strategy has limitations to accurately detect hypoxemia in children with severe pneumonia. This study will assess whether pulse oximetry improves health workers’ performance in diagnosing severe childhood pneumonia and whether the pulse oximeter is a cost-effective tool to improve diagnoses of severe pneumonia at primary health care units in South Ethiopia.Methods: A cluster-randomized controlled trial will be conducted at 24 health centres in southern Ethiopia from September 2018 to February 2019. The trial has two arms: the first arm will examine the combined use of the Integrated Management of Childhood Illness (IMCI) strategy with pulse oximetry, and the second arm will examine the use of the IMCI strategy alone. The study population will include children between 2 months and 59 months of age who present with cough or difficult breathing. The primary outcome of this trial is severe childhood pneumonia, as diagnosed via the IMCI guideline and pulse oximetry. Secondary outcomes will be referred cases of severe pneumonia, and treatment failure on day 14 after enrolment. A cost effectiveness study will be conducted simultaneously.Discussion: This study will determine if using a pulse oximeter at health facilities in rural Southern Ethiopia improves diagnostic accuracy for paediatric severe pneumonia. Our secondary aim will be to evaluate if the benefit of pulse oximetry justifies its cost. Trial registration: PACTR201807164196402(14/06/2018). URL:https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=3466. | Tesfaye SH, Gebeyehu Y, Loha E, Johansson KA, Lindtjørn B, Pulse oximeter with integrated management of childhood illness for diagnosis of severe childhood pneumonia at rural health institutions in Southern Ethiopia: results from a cluster-randomised controlled trial. BMJ Open 10(6). doi: 10.1136/bmjopen-2020-036814 | 1 School of Public Health, Hawassa University, Hawassa, Ethiopia , 2 Centre for International Health, University of Bergen, Bergen, Norway, 3 School of Public Health, Dilla University, Dilla, Ethiopia , 4 School of Medicine, Dilla University, Dilla, Ethiopia, 1 School of Public Health, Hawassa University, Hawassa, Ethiopia , 5 Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom, 2 Centre for International Health, University of Bergen, Bergen, Norway, 1 School of Public Health, Hawassa University, Hawassa, Ethiopia , 2 Centre for International Health, University of Bergen, Bergen, Norway | https://doi.org/10.1136/bmjopen-2020-036814 | 1 | 2019 | Solomon Hailemariam1, 2, 3*, Yabibal Gebeyehu4, Eskinder Loha1, 5, Kjell Arne Johansson2, Bernt Lindtjørn1, 2 2019. Improving pneumonia diagnoses using pulse oximetry at rural health institutions in southern Ethiopia: Protocol for a cluster-randomized controlled trial. protocols.io https://dx.doi.org/10.17504/protocols.io.88mhzu6 | 2021-04-15 09:14:36 | ||
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CTAB mix Resource Report Resource Website |
Andrew Baker | DOI:10.17504/protocols.io.dyt7wm | This solution is used in the coral genomic DNA extraction protocol.The following recipe is for 50 mL of CTAB mix. Store at -20°C. | Putnam HM, Davidson JM, Gates RD, Ocean acidification influences host methylation and phenotypic plasticity in environmentally susceptible corals. Evolutionary Applications 9(9). doi: 10.1111/eva.12408 | University of Miami | https://doi.org/10.1111/eva.12408 | 1 | 2016 | Andrew Baker 2016. CTAB mix. protocols.io https://dx.doi.org/10.17504/protocols.io.dyt7wm | 2021-04-15 09:14:28 | ||
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Multidisciplinary provision of food and nutritional care to hospitalised adult in-patients: A scoping review protocol Resource Report Resource Website |
Gladys Yinusa, Janet Scammell, Jane Murphy, Gráinne Ford | DOI:10.17504/protocols.io.bgzajx2e | Objective: The review will examine the evidence and characteristics of multidisciplinary care interventions in food and nutritional care provision for adult in-patients.Introduction: Providing appropriate nutritional care is fundamental in patient-centred care. Nutritional care requires a coordinated approach to the delivery of food and fluids by different healthcare professionals and the wider hospital staff. Evidence demonstrates improved patients’ clinical outcomes by enhancing hospital food and providing nutritional care throughout a patient’s pathway. While there are good examples of nutritional care initiatives, implementing appropriate nutritional care remain a challenge. Managing malnutrition particularly with adult in-patients on admission or at risk of becoming malnourished requires multidisciplinary care; the hospital team plays a crucial role in ensuring these patients’ nutritional needs are met. The review aims to identify the evidence with specific focus on reported multidisciplinary coordination and collaboration excluding artificial nutritional support (enteral and parenteral nutrition)a domain where well-established evidence already exists.Inclusion criteria: The context is limited to the hospital setting with an adult in-patient population. Studies involving healthcare professionals or the wider hospital staff will be included. Methods: Primary evidence will be included from both published and unpublished sources. The search strategy will follow the three-step process recommended by Joanna Briggs Institute’ (JBI). Data will be extracted after screening from relevant papers by two or more independent reviewers and one or more verifier using a developed data extraction tool. A narrative description of findings will be reported following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines.IntroductionKey nutrition interventions and strategies to reduce malnutrition have been recommended and some integrated into standard guidelines and policies. For instance, the recommendations for nutrition screening in routine practice to identify people with (or at risk of) malnutrition using validated malnutrition screening tools by the European Society for Clinical Nutrition and Metabolism, British Association of Parenteral and Enteral Nutrition and the National Institute for Clinical Excellence in the UK.13,14 Nutrition screening as the first step enables appropriate interventions with subsequent monitoring and assessment to be implemented. Global consensus on core diagnostic criteria for malnutrition has also been proposed to enable comparison of malnutrition prevalence, interventions, and outcomes across the world.15 Other strategies include the Protected Mealtime policy (2004) implemented in the UK aimed at avoiding all non-urgent activity on the wards during mealtimes and allowing patients to have uninterrupted meals.16 Mealtime volunteers have been shown to provide valuable support on the ward to assist with eating and drinking processes.17 However, barriers to the effective implementation of this model into practice have been reported.18,19 While supportive interventions are reported to have a beneficial effect for patients, the specific features of collaborative working approaches remain unclear.In providing nutritional care, hospital staff play a significant role in ensuring that patients’ nutritional needs are met. Some studies, guidance documents, and reports have similarly highlighted the importance of implementing an multidisciplinary approach to address the problem with the emphasis on a person-centred approach.2,21,22 The use of the term ‘nutritional care’ in this paper refers to a coordinated approach to the delivery of food and fluids by different healthcare professionals and views the patient as an individual with needs and preferences.23In a systematic review, Feinberg et al.24 reported a lack of quality evidence that examined different forms of nutrition support including general support, fortified foods, and artificial nutrition support. Rasmussen et al.25 suggested from a systematic review and meta-analysis that providing multidisciplinary nutrition support for older patients may have a positive effect on patients’ clinical outcomes, mortality and quality of life. This review sought to assess the effectiveness of multidisciplinary nutrition support studies including randomised controlled trials and excluding heterogeneous studies on multidisciplinary interventions of interest to this review. Moreover, the nature of the multidisciplinary coordinated approach merits more exploration. Evidence on the impact of complex nutritional care is well documented, including enteral or parenteral nutrition as part of artificial nutritional support for some patients.26-28 In contrast, knowledge on the coordinated delivery of other forms of nutritional care such as support for patients in the meal environment including meal support and eating support, is sparse. The present review aims to map and identify the nature of the evidence for the provision of food and nutritional care with a specific focus on reported multidisciplinary coordination and collaboration. The present study aims to map the diverse literature about multidisciplinary care and to review what has been studied and how it has been studied.Review questionsThe scoping review will be guided by this research question and the following sub-questions:What are the features of multidisciplinary collaborative care approaches implemented to improve the provision of food and nutritional care to hospitalised adult inpatients?What disciplines are involved in the multidisciplinary collaborations and what component of nutritional care are implemented? What collaborative activities, processes and outcomes of multidisciplinary nutritional care are reported? | Yinusa G, Scammell J, Murphy J, Ford G, Baron S, Multidisciplinary Provision of Food and Nutritional Care to Hospitalized Adult In-Patients: A Scoping Review. Journal of Multidisciplinary Healthcare doi: 10.2147/JMDH.S255256 | Department of Nursing Science, Faculty of Health and Social Sciences, Bournemouth University, Bournemouth United Kingdom, Department of Nursing Science, Faculty of Health and Social Sciences, Bournemouth University, Bournemouth United Kingdom, Department of Rehabilitation & Sport Sciences, Faculty of Health and Social Sciences, Bournemouth University, United Kingdom, Dietetic Department, The Royal Bournemouth and Christchurch Hospitals NHS Foundation Trust, Bournemouth United Kingdom | https://doi.org/10.2147/JMDH.S255256 | 1 | 2020 | Gladys Yinusa, Janet Scammell, Jane Murphy, Gráinne Ford 2020. Multidisciplinary provision of food and nutritional care to hospitalised adult in-patients: A scoping review protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bgzajx2e | 2021-04-15 09:14:36 | ||
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Up-regulation of vascular endothelial growth factor receptor-1 contributes to sevoflurane preconditioning mediated cardioprotection Resource Report Resource Website |
Yusheng Yao | DOI:10.17504/protocols.io.mmrc456 | Male adult Sprague–Dawley rats, weighing 270–300 g, obtained from the Animal Center of the Fujian Medical University, were anesthetized with intraperitoneal sodium pentobarbital (50 mg/kg). After intravenous injection of heparinized (50 IU) the hearts were quickly excised and fixed on a Langendorff apparatus (Radnoti, Monrovia, CA, USA) and perfused with 37°C Krebs–Henseleit buffer (KHB) at constant pressure (75 mmHg). After equilibrated with KHB for 15 min, isolated hearts were randomly divided into five groups: 1. Sham group: hearts subjected to 195-min perfusion without I/R injury; 2. I/R group: hearts received 30- min ischemia followed by 120-min reperfusion; 3. SPC group: 2.5% sevoflurane preconditioning was gived for 15 min followed by 15-min washout before ischemia; 4. SPC+MF1 group: combined application of MF1(ImClone, Somerville, NJ, USA), rat anti-VEGFR-1 monoclonal antibody,10 μmol/L and 2.5% sevoflurane preconditioning for 15 min followed by 15-min washout before ischemia; 5. SPC+PIGF group: combined application of PIGF(Abcom, Cambridge, United Kingdom)10 μmol/L and 2.5% sevoflurane preconditioning for 15 min followed by 15-min washout before ischemia. To implement sevoflurane preconditioning, the KHB was pre-equilibrated with sevoflurane under a separate reservoir with a Vapor 2000 (Dräger Medical AG & Co., Lübeck, Germany) using an air bubbler. | Qian B, Yang Y, Yao Y, Liao Y, Lin Y, Upregulation of vascular endothelial growth factor receptor-1 contributes to sevoflurane preconditioning-mediated cardioprotection. Drug Design, Development and Therapy doi: 10.2147/DDDT.S162577 | Fujian Provincial Hospital | https://doi.org/10.2147/DDDT.S162577 | 1 | 2018 | Yusheng Yao 2018. Up-regulation of vascular endothelial growth factor receptor-1 contributes to sevoflurane preconditioning mediated cardioprotection. protocols.io https://dx.doi.org/10.17504/protocols.io.mmrc456 | 2021-04-15 09:14:36 | ||
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Measurement of duodenal motility using implanted strain gauges Resource Report Resource Website |
Terry Powley, Zhenjun Tan, Matthew Ward | DOI:10.17504/protocols.io.2irgcd6 | SPARC | This protocol describes a process for the measurement of electrical stimulation-induced effects on duodenal motility in young adult Sprague-Dawley rats. Signals recorded from strain gauges attached to the proximal duodenal surface were used to measure the effect of stimulation by patch electrodes implanted at multiple sites across the rat stomach in an acute anesthetized preparation. The effect of stimulation was quantified as the ratio of various motility assessments during and after stimulation vs. before stimulation, and the data was used to create a functional map of duodenal motor response to localized gastric stimulation. | Purdue University, Purdue University, Purdue University | 1 | 2020 | Terry Powley, Zhenjun Tan, Matthew Ward 2020. Measurement of duodenal motility using implanted strain gauges. protocols.io https://dx.doi.org/10.17504/protocols.io.2irgcd6 | 2021-04-15 09:14:28 | |||
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Replacing a Bitstream at the Woods Hole Open Access Server Resource Report Resource Website |
Adam Shepherd | DOI:10.17504/protocols.io.fypbpvn | Describes how to update files at the Woods Hole Open Access Server - the institutional repository used by BCO-DMO for dataset versioning. | BCO-DMO | 1 | 2016 | Adam Shepherd 2016. Replacing a Bitstream at the Woods Hole Open Access Server. protocols.io https://dx.doi.org/10.17504/protocols.io.fypbpvn | 2021-04-15 09:14:28 | ||||
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Microorganisms and culture conditions - Comparative genomics of Staphylococcus aureus associated with subclinical and clinical bovine mastitis (Rocha et al., 2019) Resource Report Resource Website |
Lis Rocha | DOI:10.17504/protocols.io.zhrf356 | Many efforts have been made to understand the pathogenesis of bovine mastitis to reduce losses and promote animal welfare. Staphylococcus aureus may cause bovine clinical mastitis, but it is mainly associated with subclinical infection, which is usually persistent and can easily reoccur. Here, we conducted a comparative genomic analysis between four strains of S. aureus causing subclinical infection (Sau170, 302, 1269, 1364), previously sequenced by our group, and two well-characterized strains causing clinical mastitis (N305 and RF122) to find differences that could be linked to mastitis outcome. A total of 146 virulence-associated genes were compared and no appreciable differences were found between the bacteria. However, several nonsynonymous single nucleotide polymorphisms (SNPs) were identified in genes present in the subclinical strains when compared to RF122, especially in genes encoding host immune evasion and surface proteins. The comparison of orthologous genes using OrthoMCL identified a membrane transporter in the genomes of the bacteria belonging to the subclinical group, but this finding was not confirmed by polymerase chain reaction (PCR) on a collection of field isolates of S. aureus associated with clinical or subclinical mastits. The secreted and surface proteins predicted by different in silico tools were compared through multidimensional scaling analysis, revealing a high degree of similarity among the six strains. However, differences were seen in the nucleotide sequences of a gene that codes for a hypothetical protein (cl3309) and a lipoprotein (cl3700). These findings were also analyzed by PCR on DNA extracted from field isolates of S. aureus. The lipoprotein, but not the hypothetical protein, was able to separate the clinical isolates from the subclinical ones. These results show that sequence variation among bovine S. aureus, and not only the presence/absence of virulence factors, is an important aspect to consider when comparing isolates causing different mastitis outcomes | Universidade Federal de Viçosa | 2 | 2019 | Lis Rocha 2019. Microorganisms and culture conditions - Comparative genomics of Staphylococcus aureus associated with subclinical and clinical bovine mastitis (Rocha et al., 2019). protocols.io https://dx.doi.org/10.17504/protocols.io.zhrf356 | 2021-04-15 09:14:35 | ||||
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High quality DNA from Fungi for long read sequencing e.g. PacBio Resource Report Resource Website |
Benjamin Schwessinger | DOI:10.17504/protocols.io.ewtbfen | High molecular weight DNA extraction from all kingdoms, RUSTIS | Extraction of high quality DNA for long read sequencing e.g. PacBioOptimized for DNA extraction from wheat stripe rust spores and also tested on barley leaf rust.Buffers are best when fresh and not older than 3-6 months. Buffered Phenol:Chloroform:Isoamylalcohol (25:24:1) should not be older than 3 months.Critical steps to obtain high quality DNA:Do NOT heat samples during DNA extractions! Perform all steps at RT or 4oC as indicated.Do NOT incubate samples with KAc for prolonged time periodsPerform two steps of buffered Phenol:Chloroform:Isoamylalcohol purification to reduce co-purifying metabolites.DNA fragments were well above the 40kb mark based on Pippin Pulse Gels. The sequencing center performed a second AMPure purification step before library construction. Summary statistics of sequencing runs to follow. | Langner T, Harant A, Gomez-Luciano LB, Shrestha RK, Malmgren A, Latorre SM, Burbano HA, Win J, Kamoun S, Genomic rearrangements generate hypervariable mini-chromosomes in host-specific isolates of the blast fungus. PLoS Genetics 17(2). doi: 10.1371/journal.pgen.1009386 | ANU | https://doi.org/10.1371/journal.pone.0238611 | 10 | 2016 | Benjamin Schwessinger 2016. High quality DNA from Fungi for long read sequencing e.g. PacBio. protocols.io https://dx.doi.org/10.17504/protocols.io.ewtbfen | 2021-04-15 09:14:27 | |
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Salmonella Typhimurium isolation from specimens Resource Report Resource Website |
Angel Justiz-Vaillant, Suzette E. Curtello | DOI:10.17504/protocols.io.bjjdkki6 | University of the West Indies, [email protected] | Salmonella are motile, flagellated rod-shaped Zoonotic pathogens which may survive with or without oxygen and do not absorb crystal violet stain.They are decolourised by alcohol due to their outer lipopolysaccharide membrane and thin peptidoglycan layer.They belong to the family Enterobacteriaceae and is implicated with typhoid fever and food-borne illnesses.This pathogen is associated with intestinal disease which may become fatal and has negatively impact the health of individuals and various economies globally.The poultry industry is most impacted and vulnerable to the onslaught of this pernicious microbe.The Lipopolysaccharide Somatic O antigen, flagellar H and virulent V antigenic structure determines the serotype designate of Salmonella species [1]. A wide range of antisera is used in the location of the O antigen associated with the carbohydrate constituent of Lipopolysaccharide and H protein antigen linked with the flagella of the bacteria.Salmonellosis is an inflammation of the intestinal mucosal lining by Salmonella bacteria infiltration resulting in painful symptoms.Both man and animal are vulnerable.Salmonellosis is caused by ingestion of Salmonella with food (Wall et al., 1994).The main route of transmission of Salmonella microbe is fecal-oral. Ingestion of small concentration of Salmonella such as 6 cells with contaminated food or water will lead to salmonellosis infection [2].References1. Varma JK, Marcus R, Stenzel SA, et al. Highly resistant Salmonella Newport-MDRAmpC transmitted through the domestic US food supply: a FoodNet case-control study of sporadic Salmonella Newport infections, 2002-2003.J Infect Dis. 2006;194(2):222-230. doi:10.1086/505084.2. Chen W, Martinez G, Mulchandani A. Molecular beacons: a real-time polymerase chain reaction assay for detecting Salmonella.Anal Biochem. 2000;280(1):166-172. doi:10.1006/abio.2000.4518 | University of the West Indies St. Augustine, University of West Indies. Jamaica | 1 | 2020 | Angel Justiz-Vaillant, Suzette E. Curtello 2020. Salmonella Typhimurium isolation from specimens. protocols.io https://dx.doi.org/10.17504/protocols.io.bjjdkki6 | 2021-04-15 09:14:27 | |||
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MG_HW1: Starting your class project Resource Report Resource Website |
Bonnie Hurwitz | DOI:10.17504/protocols.io.fs7bnhn | Hurwitz Lab, MetaFunc Course | University of Arizona | 1 | 2016 | Bonnie Hurwitz 2016. MG_HW1: Starting your class project. protocols.io https://dx.doi.org/10.17504/protocols.io.fs7bnhn | 2021-04-15 09:14:36 | ||||
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Detection of allele frequencies in the cDNA sample Resource Report Resource Website |
Kotaro Takahagi, Komaki Inoue, Minami Shimizu, Yukiko Uehara-Yamaguchi, Yoshihiko Onda, Keiichi Mochida | DOI:10.17504/protocols.io.nafdabn | GigaScience Press | This protocol provides an useful technique for detecting allele frequencies in the cDNA sample | Takahagi K, Inoue K, Shimizu M, Uehara-Yamaguchi Y, Onda Y, Mochida K, Homoeolog-specific activation of genes for heat acclimation in the allopolyploid grass . GigaScience 7(4). doi: 10.1093/gigascience/giy020 | Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan., Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan., Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan., Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan., Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan., Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. | https://doi.org/10.1093/gigascience/giy020 | 1 | 2018 | Kotaro Takahagi, Komaki Inoue, Minami Shimizu, Yukiko Uehara-Yamaguchi, Yoshihiko Onda, Keiichi Mochida 2018. Detection of allele frequencies in the cDNA sample. protocols.io https://dx.doi.org/10.17504/protocols.io.nafdabn | 2021-04-15 09:14:32 | |
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HuBMAP UF TMC - FACS Sorting of Live Cells for 10x scRNASeq Resource Report Resource Website |
Maigan Brusko | DOI:10.17504/protocols.io.bfqzjmx6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This standard operating procedure (SOP) provides instructions for staining and sorting live cells. This SOP applies to cryopreserved cells that are stained with Live/Dead and sorted in the BD ARIA III to remove dead cells prior to 10x sequencing. | University of Florida | 1 | 2020 | Maigan Brusko 2020. HuBMAP UF TMC - FACS Sorting of Live Cells for 10x scRNASeq. protocols.io https://dx.doi.org/10.17504/protocols.io.bfqzjmx6 | 2021-04-15 09:14:36 | |||
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T Cell Activation with anti-CD3 Antibodies Protocol - Human Resource Report Resource Website |
Kelsey Knight | DOI:10.17504/protocols.io.tkbeksn | BioLegend | BioLegend | https://www.biolegend.com/protocols/t-cell-activation-with-anti-cd3-antibodies-protocol-human/4271/ | 3 | 2018 | Kelsey Knight 2018. T Cell Activation with anti-CD3 Antibodies Protocol - Human. protocols.io https://dx.doi.org/10.17504/protocols.io.tkbeksn | 2021-04-15 09:14:32 | |||
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Protocols to accompany paper entitled “Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm” Resource Report Resource Website |
Rozana Rosli, Mohd Amin Ab Halim, Chan Kuang Lim, Jayanthi Nagappan, Norazah Azizi, Faizun Kadri, Nadzirah Amiruddin, Nik Shazana Nik Mohd Sanusi, Lee Pei Lee Angel, Priscilla E Morris, Leslie Low Eng Ti, Chan Pek-Lan, Meilina Ong-Abdullah, Ravigadevi Sambanthamurthi, Rajinder Singh, Denis J Murphy | DOI:10.17504/protocols.io.mwcc7aw | Rosli R, Amiruddin N, Halim MAA, Chan P, Chan K, Azizi N, Morris PE, Low EL, Ong-Abdullah M, Sambanthamurthi R, Singh R, Murphy DJ (2018) Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm. PLoS ONE 13(4): e0194792. doi: 10.1371/journal.pone.0194792 | Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom and Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia, Genomics and Computational Biology Research Group, University of South Wales, Pontypridd, United Kingdom | https://doi.org/10.1371/journal.pone.0194792 | 1 | 2018 | Rozana Rosli, Mohd Amin Ab Halim, Chan Kuang Lim, Jayanthi Nagappan, Norazah Azizi, Faizun Kadri, Nadzirah Amiruddin, Nik Shazana Nik Mohd Sanusi, Lee Pei Lee Angel, Priscilla E Morris, Leslie Low Eng Ti, Chan Pek-Lan, Meilina Ong-Abdullah, Ravigadevi Sambanthamurthi, Rajinder Singh, Denis J Murphy 2018. Protocols to accompany paper entitled “Comparative genomic and transcriptomic analysis of selected fatty acid biosynthesis genes and CNL disease resistance genes in oil palm”. protocols.io https://dx.doi.org/10.17504/protocols.io.mwcc7aw | 2021-04-15 09:14:28 | |||
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Pi-ATAC Resource Report Resource Website |
Xingqi Chen, Ulrike Litzenburger, Yuning Wei, Alicia N. Schep, Edward L. LaGory, Hani Choudhry, Amato J. Giaccia, William J. Greenleaf, Howard Y. Chang | DOI:10.17504/protocols.io.q6gdzbw | Human Cell Atlas Method Development Community, HYChangLab | Here we introduce Protein-indexed Assay of Transposase Accessible Chromatin with sequencing (Pi-ATAC) that combines single-cell chromatin and proteomic profiling. In conjunction with DNA transposition, the levels of multiple cell surface or intracellular protein epitopes are recorded by index flow cytometry and positions in arrayed microwells, and then subject to molecular barcoding for subsequent pooled analysis. PiATAC simultaneously identifies the epigenomic and proteomic heterogeneity in individual cells. Pi-ATAC reveals a casual link between transcription factor abundance and DNA motif access, and deconvolute cell types and states in the tumor microenvironment in vivo. We identify a dominant role for hypoxia, marked by HIF1A protein, in the tumor microvenvironment for shaping the regulome in a subset of epithelial tumor cells. | Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305; Dept of Genetics, Stanford University, Stanford, CA 94305; Department of Applied Physics, Stanford University, Stanford, CA 94305, Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University, Stanford, CA 94305, Department of Biochemistry, Cancer Metabolism and Epigenetic Unit, Faculty of Science, Cancer and Mutagenesis Unit, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah, Saudi Arabia., Division of Radiation and Cancer Biology, Department of Radiation Oncology, Stanford University, Stanford, CA 94305, Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305; Dept of Genetics, Stanford University, Stanford, CA 94305; Department of Applied Physics, Stanford University, Stanford, CA 94305, Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305 | https://www.biorxiv.org/content/early/2018/04/27/310359 | 1 | 2018 | Xingqi Chen, Ulrike Litzenburger, Yuning Wei, Alicia N. Schep, Edward L. LaGory, Hani Choudhry, Amato J. Giaccia, William J. Greenleaf, Howard Y. Chang 2018. Pi-ATAC. protocols.io https://dx.doi.org/10.17504/protocols.io.q6gdzbw | 2021-04-15 09:14:26 |
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