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| Name | Authors | DOI | Group |
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Associated Publications |
RRIDs used | ||||||
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Stranded Transcript Count Table Generation from Long Reads Resource Report Resource Website |
David Eccles | DOI:10.17504/protocols.io.594g98w | This protocol is for comparing different samples at the transcript level, using long reads that are mapped to transcripts.Input(s): demultiplexed and oriented fastq files (see protocol Preparing Reads for Stranded Mapping), transcript reference fasta file, annotation fileOutput(s): transcript table, sorted by differential coverage, annotated with gene name / description / location | Malaghan Institute of Medical Research (NZ) | 8 | 2019 | David Eccles 2019. Stranded Transcript Count Table Generation from Long Reads. protocols.io https://dx.doi.org/10.17504/protocols.io.594g98w | 2021-04-15 09:15:17 | ||||
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A General Protocol for Western Blotting Mammalian Cell Lysates Resource Report Resource Website |
David Dilworth | DOI:10.17504/protocols.io.pxndpme | Structural Genomics Consortium | 1 | 2018 | David Dilworth 2018. A General Protocol for Western Blotting Mammalian Cell Lysates. protocols.io https://dx.doi.org/10.17504/protocols.io.pxndpme | 2021-04-15 09:15:17 | |||||
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Western Lysis Buffer (WLB) 250 mL Resource Report Resource Website |
Bao Thai | DOI:10.17504/protocols.io.mn7c5hn | Stephen Floor Lab | University of California, San Francisco | 1 | 2018 | Bao Thai 2018. Western Lysis Buffer (WLB) 250 mL. protocols.io https://dx.doi.org/10.17504/protocols.io.mn7c5hn | 2021-04-15 09:15:17 | ||||
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Determination of IgG concentration by the Mancini test. Resource Report Resource Website |
Angel Justiz-Vaillant | DOI:10.17504/protocols.io.bj92kr8e | University of the West Indies, [email protected] | University of the West Indies St. Augustine | 1 | 2020 | Angel Justiz-Vaillant 2020. Determination of IgG concentration by the Mancini test.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj92kr8e | 2021-04-15 09:15:45 | ||||
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Buccopharyngeal morphology of tadpoles in Scanning Electron Microscope Resource Report Resource Website |
Diogo Provete | DOI:10.17504/protocols.io.e4ebgte | 4 | 2016 | Diogo Provete 2016. Buccopharyngeal morphology of tadpoles in Scanning Electron Microscope. protocols.io https://dx.doi.org/10.17504/protocols.io.e4ebgte | 2021-04-15 09:15:17 | ||||||
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Single Amplified Genome Assembly Resource Report Resource Website |
Tyler Alioto | DOI:10.17504/protocols.io.nccdasw | SINGEK_ITN | CNAG | 1 | 2018 | Tyler Alioto 2018. Single Amplified Genome Assembly. protocols.io https://dx.doi.org/10.17504/protocols.io.nccdasw | 2021-04-15 09:15:45 | ||||
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10Xv2 RNASeq Sample Processing Resource Report Resource Website |
Allen Institute for Brain Science | DOI:10.17504/protocols.io.bq68mzhw | BICCN, Allen Institute for Brain Science | Allows for rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. | Allen Institute | 1 | 2021 | Allen Institute for Brain Science 2021. 10Xv2 RNASeq Sample Processing. protocols.io https://dx.doi.org/10.17504/protocols.io.bq68mzhw | 2021-04-15 09:15:45 | |||
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Yale - Blood and Urine Creatinine Resource Report Resource Website |
Gary Cline, John Stack | DOI:10.17504/protocols.io.y2dfya6 | Mouse Metabolic Phenotyping Centers | Procedure followed to detect the concentration of creatinine in serum, plasma, and urine. | Yale University, Yale University | https://mmpc.org/shared/document.aspx?id=204&docType=Protocol | 1 | 2019 | Gary Cline, John Stack 2019. Yale - Blood and Urine Creatinine. protocols.io https://dx.doi.org/10.17504/protocols.io.y2dfya6 | 2021-04-15 09:15:17 | ||
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pH tolerance assay for Vibrio natriegens Resource Report Resource Website |
Daniel Marchal | DOI:10.17504/protocols.io.prjdm4n | Daniel Marchal | 1 | 2018 | Daniel Marchal 2018. pH tolerance assay for Vibrio natriegens. protocols.io https://dx.doi.org/10.17504/protocols.io.prjdm4n | 2021-04-15 09:15:19 | |||||
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Staining Labyrinthulomycetes with Propidium Iodide Resource Report Resource Website |
This protocol was modified by Sabrina Geraci-Yee and is from: Pozarowski P, Darzynkiewicz Z. 2004. Analysis of cell cycle by flow cytometry. Methods Mol Bio. 281:301-311. | DOI:10.17504/protocols.io.hfjb3kn | Protist Research to Optimize Tools in Genetics (PROT-G), Collier Lab | Sabrina Geraci-Yee modified this protocol from: Pozarowski P., Darzynkiewicz Z. 2004. Analysis of cell cycle by flow cytometry. Methods Mol. Bio. 281:301-311. | , | 1 | 2017 | This protocol was modified by Sabrina Geraci-Yee and is from: Pozarowski P, Darzynkiewicz Z. 2004. Analysis of cell cycle by flow cytometry. Methods Mol Bio. 281:301-311. 2017. Staining Labyrinthulomycetes with Propidium Iodide. protocols.io https://dx.doi.org/10.17504/protocols.io.hfjb3kn | 2021-04-15 09:15:46 | |||
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U Mass - Cholesterol (LDL) Resource Report Resource Website |
Jason Kim | DOI:10.17504/protocols.io.xt9fnr6 | Mouse Metabolic Phenotyping Centers | This experiment involves a spectrophotometric measurement using Roche Cobas Clinical Chemistry Analyzer. Serum levels of LDL-cholesterol reflect cholesterol metabolism and are associated with cardiovascular disease. | University of Massachusetts | https://mmpc.org/shared/document.aspx?id=171&docType=Protocol | 1 | 2019 | Jason Kim 2019. U Mass - Cholesterol (LDL). protocols.io https://dx.doi.org/10.17504/protocols.io.xt9fnr6 | 2021-04-15 09:15:18 | ||
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Generating CB-X™ Tables and standard curves for CB-X Protein Assay Optimization Resource Report Resource Website |
G-Biosciences | DOI:10.17504/protocols.io.e4bbgsn | G-Biosciences | For routine protein assays, we recommend that researchers generate their own CB-X™ Tables or standard curves. This is a one time commitment to ensure user specific results and allows single tube assays to be performed each time as opposed to generating new calibration plots for each assay. We recommend using a protein standard similar to you protein of interest or a purified source of your protein.The supplied CB-X™ tables may result in some inconsistencies due to the type of cuvettes or microtiter plates used. CB-X™ Table for Spectrophotometer readings were measured with 1cm path length cuvettes against deionized water and CB-X™ Table for Microplate Reader readings were measured using Nunc™ Immuno 96 MicroWell™ Plates (MaxiSorp™ ) [Cat# 442404] against deionized water. | http://www.gbiosciences.com/PDF/Protocol/CB-X_Protein_Assay.pdf | 1 | 2016 | G-Biosciences 2016. Generating CB-X™ Tables and standard curves for CB-X Protein Assay Optimization. protocols.io https://dx.doi.org/10.17504/protocols.io.e4bbgsn | 2021-04-15 09:15:17 | |||
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Promega BacTiter-Glo Assay Resource Report Resource Website |
Nus Igem | DOI:10.17504/protocols.io.8ekhtcw | National University of Singapore | 1 | 2019 | Nus Igem 2019. Promega BacTiter-Glo Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.8ekhtcw | 2021-04-15 09:15:45 | |||||
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Changes in spinal stiffness with chronic thoracic pain: correlation with pain and muscle activity Resource Report Resource Website |
Isabelle Pagé, François Nougarou, Arnaud Lardon, Martin Descarreaux | DOI:10.17504/protocols.io.twwepfe | The main goal of this project is to assess the reliability of thoracic spinal stiffness. To achieve this, 25 heartily participants (no significant thoracic pain in the past year) and 25 participants with chronic thoracic pain will participate in 2 experimental sessions separated by 24 to 48 hours. These sessions will occur at the Neuromecanic and Motor Control Laboratory of the Université du Québec à Trois-Rivières (Trois-Rivières, Québec, Canada). During these sessions, spinal stiffness will be measured at four thoracic spinal levels (T5 to T8) in a randomized sequence via a mechanical device using a servo-linear motor. The device indenter (metallic cylindrical cover with a rubber of 2 cm diameter) will gradually apply 45 N to the spinous process. The muscle activity and displacement data will be recorded during the procedures. | Pagé I, Nougarou F, Lardon A, Descarreaux M (2018) Changes in spinal stiffness with chronic thoracic pain: Correlation with pain and muscle activity. PLoS ONE 13(12): e0208790. doi: 10.1371/journal.pone.0208790 | Université du Québec à Trois-Rivières, Université du Québec à Trois-Rivières, Université du Québec à Trois-Rivières, Université du Québec à Trois-Rivières | https://doi.org/10.1371/journal.pone.0208790 | 1 | 2018 | Isabelle Pagé, François Nougarou, Arnaud Lardon, Martin Descarreaux 2018. Changes in spinal stiffness with chronic thoracic pain: correlation with pain and muscle activity. protocols.io https://dx.doi.org/10.17504/protocols.io.twwepfe | 2021-04-15 09:15:45 | ||
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Detection of single nucleotide polymorphisms with padlock probes Resource Report Resource Website |
Tomasz Krzywkowski, Mats Nilsson | DOI:10.17504/protocols.io.wjhfcj6 | Molecular Diagnostics - Mats Nilsson Group, Neurodegeneration Method Development Community | This protocol is for in situ detection of mRNAs and single nucleotide polymorphisms using padlock probes and rolling circle amplification. In the accompanying publication, we take advantage of a single nucleotide variant within conserved ACTB mRNA to successfully differentiate human and mice co-cultured cells and apply following protocol to genotype PCDH X and Y homologs in human brain tissue sections. These are used as examples in the accompanying publication and custom padlock probes can be designed to allow for the targeting of own desired mRNA. We provide a method for automated characterization and quantitation of target mRNA in single cells or chosen tissue area. mRNA of interest, harboring a polymorphism, is first reverse-transcribed to cDNA. Allele specific padlock probes are hybridized to the cDNA target and enzymatically circularized maintaining a physical link with the parent mRNA molecule. Lastly, circularized probes are replicated in situ, using rolling circle amplification mechanism to facilitate detection.This protocol is taken directly from the accompanying publication. Further details and background information can be found in the cited published article. | Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden | https://link.springer.com/protocol/10.1007%2F978-1-4939-7213-5_14 | 1 | 2019 | Tomasz Krzywkowski, Mats Nilsson 2019. Detection of single nucleotide polymorphisms with padlock probes. protocols.io https://dx.doi.org/10.17504/protocols.io.wjhfcj6 | 2021-04-15 09:15:45 | ||
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Recombinant Protein Expression of MMLV-RT H+ (SkiBar H+ RT) V2 Resource Report Resource Website |
Alex Brown | DOI:10.17504/protocols.io.bijzkcp6 | Reclone.org (The Reagent Collaboration Network) | About:This protocol has been optimized for recombinant expression of molony virus based reverse transcriptases (RT). The plasmid used contains a reverse transcriptase gene which is derived from Moloney Murine Leukemia Virus. The enzyme when expressed recombinantly can synthesizes a complementary DNA strand from single-stranded RNA, DNA, or an RNA:DNA hybrid.Enzyme Engineering:The enzyme contains point mutations to generate a highly processive, thermostable, and improved fidelity mutant reverse transcriptase. Details, incluiding the sequence of this enzyme are published and can be found in the references below and addgene link. The enzyme contains an active RNAse H domain and is highly thermostable. This MMLV construct contains the following mutations: D200N, L603W, T330P, L139P, E607K,D524G, E562Q, D583N and D653N. These appear to be the same set of mutations present in the Thermo Fisher Maxima H- RT, which is one of the best preforming RTs you can buy. The enzyme in our hands is extremely active. Moreover, while the MMLV RT is thermostable and will work up to 65°C it runs optimally at 42°C.The point muitations utilized here are currently filed under a provisional patent with Thermo Fisher Scientific. Commcercial use of this enzyme must go though Thermo Fisher Scientific.It is also possible to further engineer this enzyme with to increase thermostability and eliminate RNase H activity to generate an enzyme which closely mimicks Thermo Fisher Maxima H+ RT.Introducing mutations (D524G, E562Q, D583N and D653N) and/or (D524, D583, E562, H204, V223, T306, F309) are best suted eliminate RNase H activity completely, and it will increase the thermostability somewhat as wellComments:Reference 2 highlights several point mutations which can be introduced to eliminate Rnase H activity which may also enhance RT sensitivity. Thermo Product information brochure from 2013 suggest that this mutant or some combintation of other identified point mutations from reference 2 is Maxima RT, Maxima H-. The paper has also identified a few more useful point mutations which may further optimise MMLV-RTThis expression protocol can also implemented to express other MMLV based reverse transcriptases or diversely related retroviral RTs, provided the genes are in an expresison construct with an N- terminal 6-10 His Tag and are expressed under a T7 promoter.The plasmid used can be found on reclone.org and addgeneSkiBar H+ RT was synthesized as a gBlock from IDT and is codon optimized. Expressed in Rosetta DE3 his tag is on still but seems to work fine with it on.Tgatcc motif at MCS is a result of issues cloning in with BamHI. Had to use a compatible sticky end from BclI-HFProtein Properties: 79.9 kDaIsoelectric point (pI) : 7.77Charge at pH 7.0: 9.52Name:The name SkiBar H+ RT is an abbreviation of the first two first authors where the MMLV mutations used in the construct were originally discovered (Skirgaila & Baranauskas).References:Baranauskas, Aurimas Paliksa, Sigitas Alzbutas, Gediminas Vaitkevicius, Mindaugas Lubiene, Judita Letukiene, VirginijaBurinskas, Sigitas Sasnauskas, Giedrius Skirgaila, RemigijusGeneration and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variantsProtein Engineering, Design and Selection (2012)Skirgaila, Remigijus Pudzaitis, Vaidas Paliksa, Sigitas Vaitkevicius, Mindaugas Janulaitis, ArvydasCompartmentalization of destabilized enzyme-mRNA-ribosome complexes generated by ribosome display: A novel tool for the directed evolution of enzymesProtein Engineering, Design and Selection (2013) | National Jewish Health | 2 | 2020 | Alex Brown 2020. Recombinant Protein Expression of MMLV-RT H+ (SkiBar H+ RT) V2. protocols.io https://dx.doi.org/10.17504/protocols.io.bijzkcp6 | 2021-04-15 09:15:17 | |||
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Retro-orbital Bleeding for Rats Resource Report Resource Website |
Sharona Sedighim, Olivier George | George Lab | University of California, San Diego, University of California, San Diego | 1 | 2020 | Sharona Sedighim, Olivier George 2020. Retro-orbital Bleeding for Rats. protocols.io https:// | 2021-04-15 09:15:45 | |||||
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Single Cell Seeding of BBB Stem Cell Model Resource Report Resource Website |
Ethan Lippmann, Hannah Wilson, Emma Neal | DOI:10.17504/protocols.io.8j9hur6 | Neurodegeneration Method Development Community | Standardized single cell seeding protocol for Blood-Brain Barrier (BBB) differentiation. | Department of Chemical Engineering, Vanderbilt University, Nashville, TN, USA, Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA, Department of Chemical Engineering, Vanderbilt University, Nashville, TN, USA | 1 | 2020 | Ethan Lippmann, Hannah Wilson, Emma Neal 2020. Single Cell Seeding of BBB Stem Cell Model. protocols.io https://dx.doi.org/10.17504/protocols.io.8j9hur6 | 2021-04-15 09:15:18 | |||
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Western Blotting using the Bolt system Resource Report Resource Website |
Doug Campbell, Natalie Donaher | DOI:10.17504/protocols.io.jwqcpdw | Electrophoresis and transfer steps using the Life Technologies Bolt system as done by Campbell Lab for immunoquantitation of phytoplankton proteins. | , https://sites.google.com/site/campbellphytoplankton/home | 1 | 2017 | Doug Campbell, Natalie Donaher 2017. Western Blotting using the Bolt system. protocols.io https://dx.doi.org/10.17504/protocols.io.jwqcpdw | 2021-04-15 09:15:18 | ||||
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RNA extraction for the Betta splendens genome Resource Report Resource Website |
Kailong Ma | DOI:10.17504/protocols.io.qvfdw3n | GigaScience Press, BGI | This protocol is used to clarity the process of RNA extraction for our Betta splendens genome. | BGI-Shenzhen | 1 | 2018 | Kailong Ma 2018. RNA extraction for the Betta splendens genome. protocols.io https://dx.doi.org/10.17504/protocols.io.qvfdw3n | 2021-04-15 09:15:18 |
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