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Sisbiota-Mar protocol - benthic community sampling Resource Report Resource Website |
Anaide Aued, Guilherme O. Longo | DOI:10.17504/protocols.io.p2wdqfe | The Sisbiota-mar photoquadrat survey aims to quantify the benthic cover of horizontal reef surfaces using photography and subsequent image analysis, in a manner that is directly comparable across geographies. Our survey method employs 2m2 horizontal surfaces of reef area at 1-7 meters (shallow) and 8-15 meters (deep). At each locality, between one and five reef sites were assessed (but most of them had at least three sampled sites). The 2m2 horizontal surfaces of reef area were at least 2 meters apart and haphazardly selected (avoiding sand patches). On each 2m2 reef area, the benthic community was assessed by a set of five 25x25 cm photoquadrats. | Aued AW, Smith F, Quimbayo JP, Cândido DV, Longo GO, Ferreira CEL, Witman JD, Floeter SR, Segal B (2018) Large-scale patterns of benthic marine communities in the Brazilian Province. PLoS ONE 13(6): e0198452. doi: 10.1371/journal.pone.0198452 | Universidade Federal de Santa Catarina, Universidade Federal do Rio Grande do Norte | https://doi.org/10.1371/journal.pone.0198452 | 1 | 2018 | Anaide Aued, Guilherme O. Longo 2018. Sisbiota-Mar protocol - benthic community sampling. protocols.io https://dx.doi.org/10.17504/protocols.io.p2wdqfe | 2021-04-15 09:14:26 | ||
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Loop L1 (odd level) type IIS cloning - pCk-ye vectors Resource Report Resource Website |
Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, Nicola Patron, Marta Tomaselli, Marius Rebmann, Jim Haseloff | DOI:10.17504/protocols.io.4wegxbe | OpenPlant Project | Protocol based on:Pollak B, Cerda A, Delmans M, et al (2019) Loop assembly: a simple and open system for recursive fabrication of DNA circuits. New Phytol 222:628–640https://doi.org/10.1111/nph.15625 | University of Cambridge, Plant Sciences, University of Cambridge, OpenPlant, Plant Sciences, University of Cambridge, OpenPlant, Plant Sciences, University of Cambridge, OpenPlant, University of Cambridge, Open Plant, Plant Sciences, University of Cambridge, OpenPlant, Plant Sciences, University of Cambridge, OpenPlant | 1 | 2019 | Eftychis Frangedakis, Susana Sauret-Gueto, Anthony West, Nicola Patron, Marta Tomaselli, Marius Rebmann, Jim Haseloff 2019. Loop L1 (odd level) type IIS cloning - pCk-ye vectors. protocols.io https://dx.doi.org/10.17504/protocols.io.4wegxbe | 2021-04-15 09:14:26 | |||
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SPARC Adenosine 2A Receptor Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment Resource Report Resource Website |
Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell | DOI:10.17504/protocols.io.2kfgctn | SPARC | This protocol describes the immunofluorescent labeling technique used to identify adenosine 2a receptor expression in CtB-labelled phrenic motor neurons and within a defined region of interest surrounding phrenic motor neurons. | University of Florida, University of Florida, University of Florida, University of Florida, University of Florida | 1 | 2019 | Elisa Gonzalez-Rothi, Yasin Seven, Latoya Allen, Marissa Ciesla, Gordon Mitchell 2019. SPARC Adenosine 2A Receptor Immunohistochemistry Protocol in Rat Tissues Labeled with Cholera Toxin B-fragment. protocols.io https://dx.doi.org/10.17504/protocols.io.2kfgctn | 2021-04-15 09:14:31 | |||
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Seminavis robusta protocol collection Resource Report Resource Website |
Lev Tsypin, Aaron Turkewitz | DOI:10.17504/protocols.io.4p8gvrw | Protist Research to Optimize Tools in Genetics (PROT-G) | This is a collection of media, reagents, and protocols for the cultivation and manipulation of the diatom Seminavis robusta. Our hope is that these documents will help future researchers develop genetic tools for studying this organism. | California Institute of Technology, University of Chicago | 2 | 2019 | Lev Tsypin, Aaron Turkewitz 2019. Seminavis robusta protocol collection. protocols.io https://dx.doi.org/10.17504/protocols.io.4p8gvrw | 2021-04-15 09:14:34 | |||
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Beta-glucuronidase (GUS) assay (adapted for Phaeodactylum tricornutum) Resource Report Resource Website |
Vincent A. Bielinski and Philip D. Weyman | DOI:10.17504/protocols.io.hefb3bn | Protist Research to Optimize Tools in Genetics (PROT-G) | A conventient extraction and measurement protocol for GUS activity from Phaeodactylum tricornutum. | J. Craig Venter Institute | 1 | 2017 | Vincent A. Bielinski and Philip D. Weyman 2017. Beta-glucuronidase (GUS) assay (adapted for Phaeodactylum tricornutum). protocols.io https://dx.doi.org/10.17504/protocols.io.hefb3bn | 2021-04-15 09:14:27 | |||
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Topological indexes and community structure for urban mobility networks: variations in a business day Resource Report Resource Website |
Jessica Domingues Lamosa, Lívia R Tomás, Marcos G. Quiles, Luciana R. Londe, Leonardo B L Santos, Elbert E. Macau | DOI:10.17504/protocols.io.bquwmwxe | This work fo-cused in the problem of Urban mobility, which in an unplanned urban growth sce-nario might generate negative impacts, like traffic jams, air pollution and infras-tructure flaws. Based on real data for the city of São José dos Campos, the mobil-ity of a typical day was represented. These data consist of an Origin-Destinationsurvey: the city was divided into 55 traffic zones and more than 20 thousand peo-ple were asked about the time of departure and arrival of each trip. The devel-opment was divided in 3 steps, pre-processing, processing and post-processing.In preprocessing, an origin destination graph was generated with a 3-dimensionmatrix representation, in language C++, in which each vertex represents a traf-fic zone and the edges are weighted by the flux of people, with 24 time variations,one for each hour of the day. In the processing, in C, the igraph library was usedto calculate the topological properties such as degree (number of connections),clustering coefficient (neighbors redundancy) and diameter (longest distance) ofa network of mobility over a typical day and we also applied the textit walktrapalgorithm for community detection. In the post-processing, using the concept of(geo) graphs, graphs represented with geolocation, the GeoCNet was developed. Itis a tool that allows the creation of a textit shapefile with the topological prop-erties of the graph. | Universidade Federal de São Paulo (UNIFESP), Centro Nacional de Monitoramento e Alertas de Desastres Naturais (Cemaden), Universidade Federal de São Paulo (UNIFESP), Centro Nacional de Monitoramento e Alertas de Desastres Naturais (Cemaden), Centro Nacional de Monitoramento e Alertas de Desastres Naturais (Cemaden) ; Humboldt University of Berlin, Universidade Federal de São Paulo (UNIFESP) | 3 | 2020 | Jessica Domingues Lamosa, Lívia R Tomás, Marcos G. Quiles, Luciana R. Londe, Leonardo B L Santos, Elbert E. Macau 2020. Topological indexes and community structure for urban mobility networks: variations in a business day. protocols.io https://dx.doi.org/10.17504/protocols.io.bquwmwxe | 2021-04-15 09:14:31 | ||||
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SOP Appendix for Spleen Resource Report Resource Website |
Franchesca Farris, Marda Jorgensen | DOI:10.17504/protocols.io.bcwhixb6 | Human BioMolecular Atlas Program (HuBMAP) Method Development Community | This is an appendix for spleen SOP. | University of Florida, University of Florida | 2 | 2020 | Franchesca Farris, Marda Jorgensen 2020. SOP Appendix for Spleen. protocols.io https://dx.doi.org/10.17504/protocols.io.bcwhixb6 | 2021-04-15 09:14:31 | |||
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Protocols for "Draft genome of the Tibetan medicinal herb, Rhodiola crenulata" Resource Report Resource Website |
Yuanyuan Fu, Liangwei Li, Shijie Hao, Rui Guan, Guangyi Fan, Chengcheng Shi, Haibo Wan, Wenbin Chen, He Zhang, Guocheng Liu, Jihua Wang, Lulin Ma, Jianling You, Xuemei Ni, Zhen Yue, Xun Xu, Xiao Sun, Xin Liu, Simon Ming-Yuen Lee | DOI:10.17504/protocols.io.hrkb54w | GigaScience Press | This is a collection of protocols that accompany the Yuanyuan Fu, et. al 2017 GigaScience publication "Draft genome of the Tibetan medicinal herb, Rhodiola crenulata". | Fu Y, Li L, Hao S, Guan R, Fan G, Shi C, Wan H, Chen W, Zhang H, Liu G, Wang J, Ma L, You J, Ni X, Yue Z, Xu X, Sun X, Liu X, Lee SM, Draft genome sequence of the Tibetan medicinal herb . GigaScience 6(6). doi: 10.1093/gigascience/gix033 | Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China, Institute of Chinese Medical Sciences, University of Macau, China | https://doi.org/10.1093/gigascience/gix033 | 1 | 2017 | Yuanyuan Fu, Liangwei Li, Shijie Hao, Rui Guan, Guangyi Fan, Chengcheng Shi, Haibo Wan, Wenbin Chen, He Zhang, Guocheng Liu, Jihua Wang, Lulin Ma, Jianling You, Xuemei Ni, Zhen Yue, Xun Xu, Xiao Sun, Xin Liu, Simon Ming-Yuen Lee 2017. Protocols for "Draft genome of the Tibetan medicinal herb, Rhodiola crenulata". protocols.io https://dx.doi.org/10.17504/protocols.io.hrkb54w | 2021-04-15 09:14:34 | |
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Multitissue transcriptome profiling during onset of salmon maturation Resource Report Resource Website |
Amin Mohamed, Bradley Evans, Antonio Reverter, James Kijas | DOI:10.17504/protocols.io.bnbdmai6 | Salmon Multiomics | Despite the importance of sexual maturation as a trait of interest it can be difficult to study, as the timing of onset varies widely in response to both genetics and environmental factors and occurs prior to measurable phenotypic change. To overcome this, we chose to investigate sexual maturation in Atlantic salmon where photoperiod manipulation in an experimental system can be used to synchronise animals and access tissues across the time period when animals first commit to the onset of puberty. We describe changes in genome-wide gene expression in pituitary gland, ovary and liver to identify transcriptional landscapes associated with maturation in salmon. We sequenced mRNA from four biological replicates of each tissue before (T1) and after the onset of maturation (T2, T3, T4). A total of 3.2 billion paired-end reads were mapped against the Atlantic salmon reference genome with 72% mapping efficiency to create an average depth of 50 million reads per library. The number of differentially expressed genes (DEGs) increased with elapsed time following the onset of the long light photoperiod for the two BPG axis tissues (pituitary and ovary). Of these, the ovary underwent the most dramatic remodelling over time with 403, 1709 and then 3497 DEGs observed at timepoints T2, T3 and T4 respectively. This increasing trajectory of differential ngene expression, coupled with the elevated GSI following the light stimuli, strongly suggests the experimental approach successfully initiated the onset of maturation. Next, we identified clusters of DEGs in each of the analysed tissues, which describe their physiological roles. The identity of the DEGs, in response to the onset of maturation, revealed the key players involved in the earliest triggers into maturation. Among these, upregulation of genes encoding specififc pituitary hormones such as gonadotropins along with genes encoding transcription factors (such as GATA2) are significant in controlling onset of maturation. To characterize the transcriptomic remodelling occurring in the ovary and liver, we assessed the DEG sets for GO enrichment. Upregulated genes in the ovary revealed processes related tocell adhesion, immune/inflammatory responseanddevelopment, while gene families involved inorganic acid metabolic processesandmitochondrial transportwere enriched among liver upregulated genes. This multitissue transcriptome paper provides novel insights into the transcriptional signature associated with onset of salmon maturation and is the basis of subsequent epigenetic studies aimed at understanding epigenetic mechanisms underlying maturation. | CSIRO, Tassal, CSIRO, CSIRO | 1 | 2020 | Amin Mohamed, Bradley Evans, Antonio Reverter, James Kijas 2020. Multitissue transcriptome profiling during onset of salmon maturation. protocols.io https://dx.doi.org/10.17504/protocols.io.bnbdmai6 | 2021-04-15 09:14:27 | |||
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Oil Red O Solution Resource Report Resource Website |
Sonia Hall | DOI:10.17504/protocols.io.eupbevn | University of Massachusetts Medical School | 1 | 2016 | Sonia Hall 2016. Oil Red O Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.eupbevn | 2021-04-15 09:14:31 | |||||
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16S Illumina Primer Plate Aliquoting (working plates 5µM Forw & Rev) Resource Report Resource Website |
Rodolfo Salido Benitez | DOI:10.17504/protocols.io.uz7ex9n | The following protocol outlines aliquoting resuspended primers, stored at 100µM in stock plates, into working primer plates at a conentration of 5µM for both forward (barcoded) and reverse primers, using the epMotion 5075. The Knigh Lab stores primer combos premixed in working primer plates. | Minich JJ, Humphrey G, Benitez RAS, Sanders J, Swafford A, Allen EE, Knight R, High-Throughput Miniaturized 16S rRNA Amplicon Library Preparation Reduces Costs while Preserving Microbiome Integrity. mSystems 3(6). doi: 10.1128/mSystems.00166-18 | Knight Lab @ UC San Diego Health | https://doi.org/10.1128/mSystems.00166-18 | 1 | 2018 | Rodolfo Salido Benitez 2018. 16S Illumina Primer Plate Aliquoting (working plates 5µM Forw & Rev). protocols.io https://dx.doi.org/10.17504/protocols.io.uz7ex9n | 2021-04-15 09:14:26 | ||
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Imaging on the multiworm tracker Resource Report Resource Website |
Priota Islam | DOI:10.17504/protocols.io.unpevdn | Caenorhabditis elegans, a small (adults are ~1 mm long), free-living soil nematode that feeds on bacteria, is an ideal organism for applying various live microscopy techniques. The organism is transparent, thus it is possible to microscopically analyze and record the whole animal throughout its entire life. Its complete cell lineage is known, making it possible to follow developmental and differentiation processes in real time. | Imperial College London | 1 | 2018 | Priota Islam 2018. Imaging on the multiworm tracker. protocols.io https://dx.doi.org/10.17504/protocols.io.unpevdn | 2021-04-15 09:14:31 | ||||
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Instructions for recreating the elPrep 4.0.0 WES benchmarks Resource Report Resource Website |
Charlotte Herzeel | DOI:10.17504/protocols.io.wzxff7n | This protocol describes how to recreate the elPrep 4.0.0 benchmarks for WES data. | ExaScience Life Lab, imec, Leuven, Belgium | 1 | 2019 | Charlotte Herzeel 2019. Instructions for recreating the elPrep 4.0.0 WES benchmarks. protocols.io https://dx.doi.org/10.17504/protocols.io.wzxff7n | 2021-04-15 09:14:26 | ||||
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Getting started with VirSorter2 Resource Report Resource Website |
Jiarong Guo | Ohio State University, Columbus | 1 | 2020 | Jiarong Guo 2020. Getting started with VirSorter2 . protocols.io https:// | 2021-04-15 09:14:26 | ||||||
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Multiplexed RT-qPCR to screen for SARS-COV-2 B.1.1.7, B.1.351, and P.1 variants of concern Resource Report Resource Website |
Chantal Vogels, Joseph Fauver, Nathan Grubaugh | DOI:10.17504/protocols.io.brrhm536 | Coronavirus Method Development Community | With the emergence of SARS-CoV-2 variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for targeted molecular surveillance methods. While sequencing is the gold standard, it cannot always be immediately scaled or implemented in some settings to detect variants when their frequencies are low. The Applied Biosystems TaqPath COVID-19 assay (ThermoFisher), a PCR test, was discovered to have a distinct signature (spike gene target failure, [SGTF]) when testing viruses containing the Δ69/70 HV deletion, like the B.1.1.7 variant first detected in the UK. However, a sample with a SGTF is not definitive for B.1.1.7, and cannot detect other variants of concern that lack the Δ69/70 HV deletion, such as B.1.351 detected in South Africa and P.1 recently detected in Brazil. We developed a multiplexed RT-qPCR assay that can detect all three variants by targeting the Δ3675-3677 SGF deletion in the ORF1a gene, which has not yet been widely detected in other SARS-CoV-2 lineages. Furthermore, by also targeting the Δ69/70 HV deletion in the spike gene, our assay can differentiate B.1.1.7 from B.1.351 and P.1. Finally, we include the CDC N1 primer and probe set in our multiplexed assay as a control to ensure that target failures are likely due to the presence of the ORF1a and/or spike deletions and that there is sufficient virus RNA for sequencing confirmation. Our multiplexed RT-qPCR assay can be rapidly scaled to support SARS-CoV-2 variant surveillance. .justify:after { content: ""; display:inline-block; width: 100%; } | Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Department of Epidemiology of Microbial Diseases, Yale School of Public Health | 2 | 2021 | Chantal Vogels, Joseph Fauver, Nathan Grubaugh 2021. Multiplexed RT-qPCR to screen for SARS-COV-2 B.1.1.7, B.1.351, and P.1 variants of concern. protocols.io https://dx.doi.org/10.17504/protocols.io.brrhm536 | 2021-04-15 09:14:26 | |||
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Binding properties of immunoglobulin-binding protein by double immunodiffusion (Ouchterlony) technique. Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bjqdkms6 | University of the West Indies, [email protected] | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Binding properties of immunoglobulin-binding protein by double immunodiffusion (Ouchterlony) technique. . protocols.io https://dx.doi.org/10.17504/protocols.io.bjqdkms6 | 2021-04-15 09:14:27 | ||||
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Schadenfreude is higher in real-life situations compared to hypothetical scenarios Resource Report Resource Website |
Maria Luz Gonzalez-Gadea | DOI:10.17504/protocols.io.tcbeisn | Schadenfreude (i.e., the pleasure derived from another’s misfortune) has been widely studied by having participants imagine how they would feel in hypothetical scenarios describing another person’s pain or misfortune. However, research on affective forecasting shows that self-judgments of emotions are inaccurate in hypothetical situations. Here we show a study in which we first presented a hypothetical schadenfreude situation and few months later, due to an exceptional circumstance, the situation turned out to happen in reality. This fortuitous circumstance allowed us to compare people’s imagined emotional reactions with their actual feelings. Results showed that schadenfreude was higher in the real situation than in the hypothetical one. More importantly, participants used different proxies to predict their emotional reaction: while out-group dislike served as a proxy of schadenfreude in both types of scenario, the degree of in-group identification also increased schadenfreude in those who had experienced the real event, arguably a mechanism to promote positive self-evaluation. These results highlight the importance of assessing schadenfreude in the heat of the moment. | Gonzalez-Gadea ML, Ibanez A, Sigman M (2018) Schadenfreude is higher in real-life situations compared to hypothetical scenarios. PLoS ONE 13(10): e0205595. doi: 10.1371/journal.pone.0205595 | 1. Laboratory of Neuroscience, Torcuato di Tella University | https://doi.org/10.1371/journal.pone.0205595 | 2 | 2018 | Maria Luz Gonzalez-Gadea 2018. Schadenfreude is higher in real-life situations compared to hypothetical scenarios. protocols.io https://dx.doi.org/10.17504/protocols.io.tcbeisn | 2021-04-15 09:14:31 | ||
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Zobell Agar/Broth Medium Resource Report Resource Website |
Shalaja Srinagesh et al | DOI:10.17504/protocols.io.dbn2md | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Shalaja Srinagesh et al 2016. Zobell Agar/Broth Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbn2md | 2021-04-15 09:14:33 | ||||
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Script P7: Assigning Whole Metagenome Taxonomy Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.egubbww | VERVE Net, Club Grice | This protocol provides a method for assigning whole metagenome taxonomy using MetaPhlAn and MEGAN toolkits. Based on the methods from the following publication:Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script P7: Assigning Whole Metagenome Taxonomy. protocols.io https://dx.doi.org/10.17504/protocols.io.egubbww | 2021-04-15 09:14:26 | |
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Reproducibility for Thistlethwaite et al. 2020 Resource Report Resource Website |
Lillian Thistlethwaite, xiqi.li2 , Varduhipetrosyan | DOI:10.17504/protocols.io.bpdvmi66 | Metabolomics Protocols & Workflows | We consider the following algorithmic problem that arises in transcriptomics, metabolomics and other fields: given a weighted graph and a subset of its nodes, find subsets of perturbed variables that show significant connectedness within the graph. While solutions to this problem may be discovered by devising a variety of scoring functions, statistically rigorous discovery is obstructed by the high computational cost of permutation testing, required to establish p-values. In this work, we develop CTD, a novel information-theoretic method that evaluates the connectedness of perturbation signatures in a network context and assigns an upper bounds on their p-values without use of permutation testing. We apply CTD to interpret multi-metabolite perturbations due to inborn errors of metabolism and multi-gene perturbations associated with breast cancer in the context of disease-specific Gaussian Markov Random Field networks learned directly from respective molecular profiling data. | Thistlethwaite LR, Petrosyan V, Li X, Miller MJ, Elsea SH, Milosavljevic A (2021) CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models. PLoS Comput Biol 17(1): e1008550. doi: 10.1371/journal.pcbi.1008550 | Baylor College of Medicine, Baylor College of Medicine, Baylor College of Medicine | https://doi.org/10.1371/journal.pcbi.1008550 | 4 | 2020 | Lillian Thistlethwaite, xiqi.li2 , Varduhipetrosyan 2020. Reproducibility for Thistlethwaite et al. 2020. protocols.io https://dx.doi.org/10.17504/protocols.io.bpdvmi66 | 2021-04-15 09:14:27 |
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