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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Re-amplification of CRISPRa and CRISPRi libraries (v1.0)Reference: Genome-Scale CRISPR-Mediated Control of Gene Repression and A Resource Report Resource Website |
IGI | 10.17504/protocols.io.dmz475 | CornLab | 1 | 2015 | IGI 2015. Re-amplification of CRISPRa and CRISPRi libraries (v1.0)Reference: Genome-Scale CRISPR-Mediated Control of Gene Repression and A. protocols.io dx.doi.org/10.17504/protocols.io.dmz475 | 2021-03-29 03:09:22 | |||||
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Determining Genome Targeting Efficiency using T7 Endonuclease I (M0302) Resource Report Resource Website |
Breton Hornblower | 10.17504/protocols.io.eqxbdxn | T7 Endonuclease I recognizes and cleaves non-perfectly matched DNA. This protocol describes how to determine genome targeting efficiency by digesting annealed PCR products with T7 Endonuclease I. In the first step PCR products are produced from the genomic DNA of cells whose genomes were targeted using Cas9, TALEN, ZFN etc. In the second step, the PCR products are annealed and digested with T7 Endonuclease I. Fragments are analyzed to determine the efficiency of genome targeting. | New England Biolabs | https://www.neb.com/protocols/2014/08/11/determining-genome-targeting-efficiency-using-t7-endonuclease-i | 2 | 2016 | Breton Hornblower 2016. Determining Genome Targeting Efficiency using T7 Endonuclease I (M0302). protocols.io dx.doi.org/10.17504/protocols.io.eqxbdxn | 2021-03-29 03:09:21 | |||
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Zymo Research DNA Clean & Concentrator Resource Report Resource Website |
Alan Cone | 10.17504/protocols.io.egbbbsn | Ju Lab | Cleans and concentrates any DNA. Typically useful after PCR, restriction digest, or anything where DNA was altered and now you need your newly altered DNA in a pure form. | Wright State University | 1 | 2016 | Alan Cone 2016. Zymo Research DNA Clean & Concentrator. protocols.io dx.doi.org/10.17504/protocols.io.egbbbsn | 2021-03-29 03:09:22 | |||
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U Mass - Creatinine Resource Report Resource Website |
Jason Kim | 10.17504/protocols.io.xvjfn4n | Mouse Metabolic Phenotyping Centers | This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Serum levels of creatinine reflect systemic protein metabolism. | University of Massachusetts | https://mmpc.org/shared/document.aspx?id=184&docType=Protocol | 1 | 2019 | Jason Kim 2019. U Mass - Creatinine. protocols.io dx.doi.org/10.17504/protocols.io.xvjfn4n | 2021-03-29 03:09:22 | ||
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Preparation of M9 Media Resource Report Resource Website |
Nus Igem | 10.17504/protocols.io.8cjhsun | National University of Singapore | 2 | 2019 | Nus Igem 2019. Preparation of M9 Media. protocols.io dx.doi.org/10.17504/protocols.io.8cjhsun | 2021-03-29 03:09:21 | |||||
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Effect of different types of non-invasive central nervous system stimulation on pain perception, cortical and spinal cord excitability in healthy individuals. Resource Report Resource Website |
Plínio Luna de Albuquerque | 10.17504/protocols.io.nkidcue | It is a crossover, double-blind, sham-controlled, pseudorandomized, and counterbalanced study at the Laboratory of Applied Neuroscience (LANA) of the Federal University of Pernambuco (UFPE). We performed a double-blind, randomized, sham-controlled crossover study with 12 healthy volunteers who underwent single sessions of rTMS (1Hz, 20Hz and Sham) and tsDCS (anodal, cathodal and Sham) associated with 20 minutes of treadmill walking. Cortical excitability was assessed by motor evoked potential (MEP) and spinal cord excitability by the Hoffmann reflex (Hr), nociceptive flexion reflex (NFR) and homosynaptic depression (HD). All measures were assessed before, immediately, 30 and 60 minutes after the experimental procedures. | Albuquerque PL, Campêlo M, Mendonça T, Fontes LAM, Brito RdM, Monte-Silva K (2018) Effects of repetitive transcranial magnetic stimulation and trans-spinal direct current stimulation associated with treadmill exercise in spinal cord and cortical excitability of healthy subjects: A triple-blind, randomized and sham-controlled study. PLoS ONE 13(3): e0195276. doi: 10.1371/journal.pone.0195276 | Applied Neuroscience Laboratory, Department of Physical Therapy, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil. | https://doi.org/10.1371/journal.pone.0195276 | 1 | 2018 | Plínio Luna de Albuquerque 2018. Effect of different types of non-invasive central nervous system stimulation on pain perception, cortical and spinal cord excitability in healthy individuals.. protocols.io dx.doi.org/10.17504/protocols.io.nkidcue | 2021-03-29 03:09:21 | ||
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Carbon and nitrogen stable isotope analysis in harbor seal pup fur at CICESE Resource Report Resource Website |
Juan Carlos Herguera-García, Gisela Heckel | 10.17504/protocols.io.2m3gc8n | In the Stable Isotope Laboratory at CICESE (Ensenada Center for Scientific Research and Graduate Education, Mexico) animal tissues (pup fur from Pacific harbor seals, Phoca vitulina richardii) were ground for isotopic determinations. Samples were stored in a dissecator until they were loaded into a Costech® Carrousel. Samples were combusted at high temperature (1000˚C) in a pure oxygen atmosphere in an elemental analyzer coupled to a Finnigan MAT Delta V Advantage continuous flow stable isotope mass spectrometer.Stable carbon and nitrogen ratios are expressed as δ13C or δ15N according to the following equation:δ13C or δ15N (‰) = [Rsample/Rstandard)–1]* 1000 (1) where R is 13C/ 12C or 15N/ 14N. Isotopic values of carbon and nitrogen are reported relative to Pee Dee Belemnite and atmospheric nitrogen standards, respectively. The accuracy of isotopic measurements was verified using secondary standard reference materials (Glutamic acid, a pure carbonate Merck and the laboratory internal references Lanugo for N, and CH94 for C). | Juárez-Rodríguez M, Heckel G, Herguera-García JC, Elorriaga-Verplancken FR, Herzka SZ, Schramm Y (2020) Trophic ecology of Mexican Pacific harbor seal colonies using carbon and nitrogen stable isotopes. PLoS ONE 15(1): e0225889. doi: 10.1371/journal.pone.0225889 | Centro de Investigación Científica y de Educación Superior de Ensenada, Mexico (CICESE), Centro de Investigación Científica y de Educación Superior de Ensenada, Mexico (CICESE) | https://doi.org/10.1371/journal.pone.0225889 | 1 | 2019 | Juan Carlos Herguera-García, Gisela Heckel 2019. Carbon and nitrogen stable isotope analysis in harbor seal pup fur at CICESE. protocols.io dx.doi.org/10.17504/protocols.io.2m3gc8n | 2021-03-29 03:09:21 | ||
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Heat fragmented genomic DNA before Illumina library preparation for sequencing GC rich fraction of heterogeneous genome Resource Report Resource Website |
Marie-Ka Tilak | 10.17504/protocols.io.jxicpke | This protocol was developed with the aim of sequencing the GC rich part of heterogeneous genomes with the Illumina technology. To this aim, fragmented genomic DNA is denaturized up to 90°C before library preparation. This procedure enriches the library in GC-rich fragments and leads to a substantial increase in average GC content of sequence reads. | Tilak M, Botero-Castro F, Galtier N, Nabholz B, Illumina Library Preparation for Sequencing the GC-Rich Fraction of Heterogeneous Genomic DNA. Genome Biology and Evolution 10(2). doi: 10.1093/gbe/evy022 | 1 Institut des Sciences de l'Evolution de Montpellier (ISE-M) UMR 5554 Université de Montpellier - Centre National de la Recherche Scientifique - Institut de Recherche pour le Développement – École Pratique des Hautes Études | https://doi.org/10.1093/gbe/evy022 | 1 | 2017 | Marie-Ka Tilak 2017. Heat fragmented genomic DNA before Illumina library preparation for sequencing GC rich fraction of heterogeneous genome . protocols.io dx.doi.org/10.17504/protocols.io.jxicpke | 2021-03-29 03:09:22 | ||
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Electrocompetent Agrobacterium transformation Resource Report Resource Website |
Magdalena Julkowska | 10.17504/protocols.io.pewdjfe | Salt Lab KAUST | Standard protocol for Agrobacterium transformation | King Abdullah University of Science and Technology | 1 | 2019 | Magdalena Julkowska 2019. Electrocompetent Agrobacterium transformation. protocols.io dx.doi.org/10.17504/protocols.io.pewdjfe | 2021-03-29 03:09:22 | |||
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How to copy from host to guest machine Resource Report Resource Website |
James Thornton | 10.17504/protocols.io.ferbjd6 | ECOGEO | Short instructions on how to allow copying and pasting to the virtual machine. | EARTHCUBE OCEANOGRAPHY AND GEOBIOLOGY ENVIRONMENTAL 'OMICS | 1 | 2016 | James Thornton 2016. How to copy from host to guest machine. protocols.io dx.doi.org/10.17504/protocols.io.ferbjd6 | 2021-03-29 03:09:22 | |||
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Quantitative PCR analysis to assess gene expression changes in hyperglycemic larval zebrafish Resource Report Resource Website |
Sandra Rieger | 10.17504/protocols.io.3bagiie | Diabetic Complications Consortium | To assess hyperglycemia in larval zebrafish, we analyzed the expression of genes implicated in glucose metabolism, such as insulin, insulin receptor, glucagon, and phosphoenolpyruvate carboxylase (pepck), using quantitative PCR (qPCR). We analyzed gene expression following treatment of Tg(ins:NTRmCherry) transgenic larvae either with 0.5 % DMSO (controls) or 10 mM metronidazole (see Protocol 2) for β-cell ablation at 3 and 8 days post fertilization (dpf). Diabetic Complication: | University of Miami | https://www.diacomp.org/shared/document.aspx?id=222&docType=Protocol | 1 | 2019 | Sandra Rieger 2019. Quantitative PCR analysis to assess gene expression changes in hyperglycemic larval zebrafish. protocols.io dx.doi.org/10.17504/protocols.io.3bagiie | 2021-03-29 03:09:22 | ||
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BioMark Single Cell Protocol (Two-Step RTSTA) Resource Report Resource Website |
Shaina Robbins, Alison Moss, Sean Nieves | 10.17504/protocols.io.wdsfa6e | SPARC | This protocol utilizes Fluidigm's Biomark system which performs high-throughput real-time PCR that can assay 48 or 96 genes for 48 or 96 samples respectfully. This protocol is used for gene expression targeting samples at the single-cell scale and can be used with the 48.48 Dynamic Array integrated fluidic circuit (IFC) or the 96.96 Dynamic Array IFC. Note that this protocol assumes that single-cell samples are captured using the Arcturus Laser Capture Microdissection system. | Thomas Jefferson University, Thomas Jefferson University, Thomas Jefferson University | 1 | 2020 | Shaina Robbins, Alison Moss, Sean Nieves 2020. BioMark Single Cell Protocol (Two-Step RTSTA). protocols.io dx.doi.org/10.17504/protocols.io.wdsfa6e | 2021-03-29 03:09:23 | |||
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Golden Gate plasmids used for transfection of Perkinsus marinus Resource Report Resource Website |
Elin Einarsson | 10.17504/protocols.io.37egrje | Protist Research to Optimize Tools in Genetics (PROT-G) | We have created plasmids for transfection of the parasite Perkinsus marinus using Golden Gate cloning. We have explored the possibility to either FACS sort (GFP/mCherry fused to MOE membrane protein) or using drug selection (bleomycin, blasticidin S or puromycin) to enrich transfected cells. | Waller Lab, Department of Biochemistry, University of Cambridge | 1 | 2019 | Elin Einarsson 2019. Golden Gate plasmids used for transfection of Perkinsus marinus. protocols.io dx.doi.org/10.17504/protocols.io.37egrje | 2021-03-29 03:09:23 | |||
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DNA construct for genetic transformation of the coral symbiotic alga Breviolum sp. Resource Report Resource Website |
Jun Minagawa | 10.17504/protocols.io.7udhns6 | National Institute for Basic Biology | 1 | 2019 | Jun Minagawa 2019. DNA construct for genetic transformation of the coral symbiotic alga Breviolum sp.. protocols.io dx.doi.org/10.17504/protocols.io.7udhns6 | 2021-03-29 03:09:23 | |||||
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Growth of Dunaliella salina on artificial seawater. Resource Report Resource Website |
Larry Klobutcher | 10.17504/protocols.io.gwpbxdn | Protist Research to Optimize Tools in Genetics (PROT-G) | University of Connecticut, School of medicine | 1 | 2017 | Larry Klobutcher 2017. Growth of Dunaliella salina on artificial seawater.. protocols.io dx.doi.org/10.17504/protocols.io.gwpbxdn | 2021-03-29 03:09:20 | ||||
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U Cinn - Triglyceride Assay Resource Report Resource Website |
Patrick Tso, Dana Lee | 10.17504/protocols.io.xm4fk8w | Mouse Metabolic Phenotyping Centers | Determinations of triglycerides in plasma/serum/lymph will be made using a Randox Triglycerides colorimetric kit. The triglycerides are determined after enzymatic hydrolysis with lipases. | University of Cincinnati, University of Cincinnati | https://mmpc.org/shared/document.aspx?id=200&docType=Protocol | 1 | 2019 | Patrick Tso, Dana Lee 2019. U Cinn - Triglyceride Assay. protocols.io dx.doi.org/10.17504/protocols.io.xm4fk8w | 2021-03-29 03:09:22 | ||
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gRNA design and cloning with BbsI into Loop plasmid L1_lacZgRNA-Ck2/3 Resource Report Resource Website |
Eftychis Frangedakis, Marta Tomaselli, Susana Sauret-Gueto | 10.17504/protocols.io.94ah8se | OpenPlant Project | This protocol explains how to design and clone the guide RNA target sequence into a L1 plasmid ready to accept the gRNA by cloning with BbsI. L1 plasmids are L1_lacZgRNA-Ck2 and L1_lacZgRNA-Ck3.If one gRNA target sequence is cloned into the Ck2 plasmid and another one into Ck3 one, the two L1_gRNA transcription units can be combined with an antibiotic resistance transcription unit and a MpEF1α:Cas9 transcription unit via L2 SapI Loop assembly. This allows for dual gRNA editing. | University of Cambridge, Plant Sciences, University of Cambridge, OpenPlant, Plant Sciences, University of Cambridge, OpenPlant | 1 | 2019 | Eftychis Frangedakis, Marta Tomaselli, Susana Sauret-Gueto 2019. gRNA design and cloning with BbsI into Loop plasmid L1_lacZgRNA-Ck2/3. protocols.io dx.doi.org/10.17504/protocols.io.94ah8se | 2021-03-29 03:09:22 | |||
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Plating Prochlorococcus and Synechococcus strains in top agarose for plaque assays Resource Report Resource Website |
Matthew Sullivan | 10.17504/protocols.io.c3vyn5 | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Plating Prochlorococcus and Synechococcus strains in top agarose for plaque assays. protocols.io dx.doi.org/10.17504/protocols.io.c3vyn5 | 2021-03-29 03:09:22 | ||||
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Blood Pressure Measurement: Kent Coda 8 (Tail-Cuff) Resource Report Resource Website |
Deborah A. Howatt, Anju Balakrishnan, Hong Lu | 10.17504/protocols.io.iygcftw | Sangderk Lee lab | Kim S, Yang L, Kim S, Lee RG, Graham MJ, Berliner JA, Lusis AJ, Cai L, Temel RE, Rateri DL, Lee S (2017) Targeting hepatic heparin-binding EGF-like growth factor (HB-EGF) induces anti-hyperlipidemia leading to reduction of angiotensin II-induced aneurysm development. PLoS ONE 12(8): e0182566. doi: 10.1371/journal.pone.0182566 | DAUGHERTY LAB, Cardiovascular Research Center, University of Kentucky, DAUGHERTY LAB, Cardiovascular Research Center, University of Kentucky, DAUGHERTY LAB, Cardiovascular Research Center, University of Kentucky | https://doi.org/10.1371/journal.pone.0182566 | 2 | 2017 | Deborah A. Howatt, Anju Balakrishnan, Hong Lu 2017. Blood Pressure Measurement: Kent Coda 8 (Tail-Cuff). protocols.io dx.doi.org/10.17504/protocols.io.iygcftw | 2021-03-29 03:09:23 | ||
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Vegetation Monitoring Protocol for measuring and collecting ecological data Resource Report Resource Website |
Rebecca Hufft, Christina Alba, Amy Sahud | 10.17504/protocols.io.bkfuktnw | This protocol outlines the basic methods for measuring understory percent cover, soil moisture, tree canopy cover, and plant species richness, as well as for collecting plant specimens to be vouchered in the herbarium. These measurements estimate the abundance and presence of plant species in an area, and link them to environmental conditions (soil water and light availability) that may affect their distributions. Together, these data can reveal patterns in plant community or ecosystem processes.The understory percent cover measurements will be made using the line-point intercept method. In this method, a 25m transect is placed along the ground with a 25m by 1m belt transect to either side of it. Percent cover is measured along the transect, along with soil moisture and tree canopy cover. Plant richness is measured in the belt transect and the plant vouchering is done outside of the transect and belt transect area. | Denver Botanic Gardens, Denver Botanic Gardens, Denver Botanic Gardens | www.botanicgardens.org | 1 | 2020 | Rebecca Hufft, Christina Alba, Amy Sahud 2020. Vegetation Monitoring Protocol for measuring and collecting ecological data. protocols.io dx.doi.org/10.17504/protocols.io.bkfuktnw | 2021-03-29 03:09:20 |
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