http://www.alexandergarcia.name/ sp http://oxgiraldo.wordpress.com/ http://purl.org/net/SMARTprotocol# SMART Protocols Ontology: Document Module 2013-07-01 SMART Protocols Ontology: Document Module is an ontology designed to represent metadata used to report an experimental protocol. 4.0 SMART Protocols Ontology: Document Module http://creativecommons.org/licenses/by/4.0/ http://www.dia.fi.upm.es/index.php?page=oscar-corcho/ SMART Protocols Ontology: Document Module is an ontology designed to represent metadata used to report an experimental protocol. A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not example of usage The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. definition An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) alternative term formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 definition source For external terms/classes, the ontology from which the term was imported imported from The property has concentration relates a molecular entity, compound, substance, reagent or solute present in a unit amount of mixture. has concentration http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities) c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. has_manufacturer OBI is manufactured by this cell derives from this parent cell (cell division); this nucleus derives from this parent nucleus (nuclear division). derives from is a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity. derives_from ro.owl derives from First name of a person OCRe has first name Last name of a person OCRe has last name The property acceptedBy indicates the person or authoritative body who, after theprocess of validation of a protocol, accepts the modifications made to this document before to its massive implementation. accepted by the property adaptedFrom is the retationship that binds a protocol to a provenance of the protocol adapted from hasAdvantage is a relation that binds an experimental protocol to an advantage of the protocol. has advantage "DNA Extraction Protocol" hasAlertMessage "Critical Step" hasAlertMessage is a relation that binds a chemical substance or protocol to an alert message such as caution, critical step, timing, etc. has alert message The property hasAnnealingTemperature indicates the temperature allowing annealing of the primers to the single-stranded DNA template during a PCR. The temperature should be from 42-65°C. has melting temperature has annealing temperature The property hasAnnealingTime indicates the time allowing annealing of the primers to the single-stranded DNA template during a PCR. Typical annealing times are 15-30 seconds. has melting time has annealing time hasApplication is a relation that binds a document such as experimental protocol to a application of the protocol. has application "Laboratory protocol" hasAuthor "John Smith" hasAuthor is a relation that binds a document such as experimental protocol to an author has author hasAuthorIdentification is a relation that binds an author to an author identifier. has author identification "Nalgene Cryogenic Tube" hasCatalogNumber "5000-0012" hasCatalogNumber is a relation that binds a material entity to a numeral or string of numerals that is used for identification. has catalog number hasDevelopmentalStage is a relation that binds a specimen to an developmental stage. has developmental stage hasExperimentalInput is a relation that binds a experimental protocol to a material entity participating in a protocol. has experimental input The property hasFinalConcentration relates the final measured concentration of a molecular entity, compound, substance, reagent or solute and the class final concentration. has final concentration hasGrowthConditions is a relation that binds a specimen entry to an growth conditions entry has growth conditions hasIdentifier is a relation that binds a document such as an experimental protocol to an protocol identifier has identifier The property hasInitialConcentration relates the first measured concentration of a molecular entity, compound, substance, reagent or solute and the class initial concentration. has initial concentration hasInstruction is a relation that binds a experimental protocol to a protocol instruction. has instruction hasLimitation is a relation that binds a document such as experimental protocol to a limitation of protocol. has limitation "Buffer" hasName "1X Queen’s lysis buffer (1L)" hasName binds to a person, animal, place or thing to a word or set of words by which someone or something is known, addressed, or referred to. has name hasOutcome is a relation that binds a document such as experimental protocol to an outcome of the protocol. has outcome The property primerLength indicates the length of PCR primers. This length is long enough for adequate specificity and short enough for primers to bind easily to the template at the annealing temperature. The typical length of PCR primers is 18-30bp. has primer length hasPurpose is a relation that binds a document such as experimental protocol to an purpose of the protocol. has purpose The property hasQuantity indicates how much there is of something that you can measure; the total amount or number. has quantity The primer CII-fw hasSequence 5′-GAATGATGTACCACCTTTG-3′ hasSequence is a relation that binds a oligonucleotide or nucleic acid to a sequence. has sequence hasSpecimenTreatment is a relation that binds a specimen to a specimen treatment protocol has sample treatment has specimen treatment The property hasSubject indicates the topic or topics of a resource, for example a protocol. has subject has technique "Laboratory protocol" hasTitle "An Optimized Chloroplast DNA Extraction Protocol for Grasses (Poaceae) Proves Suitable for Whole Plastid Genome Sequencing and SNP Detection" hasTitle is a relation that binds a document such as laboratory protocol to a title of protocol. has title the property publishedIn is the retationship that binds a Protocol to a RepositoryName located in The property modifiedBy indicates the person or authoritative body who changed an item, for example, a protocol. edited by modified by the property publishedIn is the retationship that binds a protocol to a publicationName published in title of The property validatedBy indicates the person who formally assesses or examines that the protocol can be understood and carried out correctly by users. validated by PAV ontology has current version PAV ontology has version the experimental protocol A was created by B author. has creator is a relation between an entity, such as, an author and the protocol that this person have created. was created by is created by Semanticscience Integrated Ontology has creator OBI has part Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. OBO Relation Ontology part of a plant variety obtained in agriculture in horticulture. Microarray and Gene Expression Data Ontology (MGEDO) cultivar a biotype resulting from selection in a particular habitat, e.g. the A. thaliana Ecotype Ler Microarray and Gene Expression Data Ontology (MGEDO) ecotype A strain or line is an animal or plant offspring that has a single ancestral breeding pair or parent as a result of brother x sister or parent x offspring matings. This class is extended to include F1 offspring and established breeding lines. For microbes, these are isolates derived from nature or in the laboratory. organism strain organism line Microarray and Gene Expression Data Ontology (MGEDO) strain or line An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function. CDISC NCI thesaurus tissue The quantity of a substance per unit volume or weight; a measure of the amount of substance present in a unit amount of mixture, particularly, the amount of solute dissolved in a solvent. The amounts can be expressed as moles, masses, volumes, or parts. NCI thesaurus concentration The words or language units by which a thing is known. NCI thesaurus name A message describing how something is to be done. step NCIT Instruction instruction An aqueous dilution of ethanol containing 70% ethanol by volume. 70% Ethyl Alcohol Ethyl Alcohol, 70% Alcohol, Ethyl 70% 70% (v/v) ethanol 70 per cent alcohol 70% RNase-free ethanol 70% RNase free ethanol 70% EtOH NCIThesaurus 70% Ethanol A homogeneous mixture of two or more substances; frequently (but not necessarily) a liquid solution. NCI thesaurus solution The first measured concentration of a compound in a substance. In pharmacology, the initial concentration is given only for bolus IV models. NCI thesaurus initial concentration Date on the cover of a magazine issue, suitable for storing in a database field with a 'date' data type. PRISM The cover date on a magazine indicates the last date the printed issue should be displayed for sale, NOT the publication date as commonly believed. Not applicable to non-print platforms. cover date An element used to tag keywords that are likely to be used in search queries. PRISM Note that this differs from a subject or elements such as dc:subject, prism:person, prism:event, or prism:organization that are the subject of the article. Best practice is to use values from a keyword controlled vocabulary for this element keyword Title of the magazine, or other publication, in which a resource was/will be published. repository name PRISM publication name tissue and cells derived from animals for use in research. nonhuman tissue CRISP animal tissue a ubiquitous tissue culture model for nontransformed animal cells; derived from nonneoplastic immortalized fibroblasts. CRISP 3T3 cell Expendable and nonexpendable equipment, supplies, apparatus, and instruments that are used in diagnostic, surgical, therapeutic, scientific, and experimental procedures. Device Apparatus and Instruments Device, Medical Devices, Medical Instruments and Apparatus Inventory Medical Device Supplies and Equipment MED DEVICE EQUIPMENT SUPPLIES MED DEVICES APPARATUS INSTRUM DEVICES MED DEVICE MED Devices Equipment Inventories Medical Devices Supplies Medical Subject Headings (MeSH) equipment and supplies NCBITaxon Trypanozoon NCBITaxon Nannomonas Trypanosoma is a genus of kinetoplastids (class Kinetoplastida), a monophyletic group of unicellular parasitic flagellate protozoa. https://en.wikipedia.org/wiki/Trypanosoma NCBITaxon Trypanosoma Trypanosoma (Trypanozoon) brucei Trypanosoma brucei subgroup NCBITaxon Trypanosoma brucei T. congolense NCBITaxon Trypanosoma congolense SNOMEDCT bacterial cell A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. BFO role Established from a human primary embryonal kidney transformed by adenovirus type 5. A293 cell HEK cell 293 cell A-293 cell HEK293 cell human embryonic kidney cell human embryonal kidney cell cell line ontology (CLO) HEK-293 cell Brenda Tissue Ontology embryonic cell line Very widely used mouse fibroblast cell line; 3T3 cells have been derived from different mouse strains and it is therefore important to define the particular cell line. NIH strain were from the National Institute of Health in the USA; Mouse embryonic fibroblast cell line, established from disaggregated Swiss albino mouse embryos in 1962. 3T3-Swiss albino cell NIH 3T3 cell 3T3 cell NIH3T3 cell 3T3 fibroblast NIH/3T3 cell Brenda Tissue Ontology NIH-3T3 cell Brenda Tissue Ontology embryonic kidney cell line Brenda Tissue Ontology embryonic fibroblast an alkanesulfonate that has formula C32H58N2O7S. C32H58N2O7S 3-((3-Cholamidopropyl)dimethylammonium)-1-propanesulfonate CHEBI CHAPS Aldehydic parent sugars (polyhydroxy aldehydes H[CH(OH)]nC(=O)H, n >= 2) and their intramolecular hemiacetals. C2H4O2(CH2O)n an aldose aldoses Aldose CHEBI aldose CHEBI primary alcohol An organic hydroxy compound that consists of benzene bearing a single hydroxy substituent. The parent of the class of phenols. Hydroxybenzene carbolic acid acide phenique C6H6O Phenic acid Phenylic acid acide carbolique Benzenol Phenylic alcohol PhOH Carbolsaeure Oxybenzene Karbolsaeure CHEBI phenol A primary alcohol that is ethane in which one of the hydrogens is substituted by a hydroxy group. OXYDIMETHYLENE GROUP Aethylalkohol Ethyl alcohol Aethanol spiritus vini hydroxyethane EtOH 1-hydroxyethane etanol Methylcarbinol alcool ethylique alcohol etilico alcohol Dehydrated ethanol C2H6O [OEtH] [CH2Me(OH)] CCO C2H5OH Alkohol CHEBI ethanol A monohydroxy-5beta-cholanic acid with a alpha-hydroxy substituent at position 3. It is a bile acid obtained from chenodeoxycholic acid by bacterial action. 3c-5beta-cholan-24-oic acid Lithocholic acid C24H40O3 3alpha-Hydroxy-5beta-cholanic acid (3alpha,5beta)-3-hydroxycholan-24-oic acid 3alpha-hydroxy-5beta-cholanoic acid 3alpha-hydroxy-5beta-cholanic acid 3alpha-Hydroxy-5beta-cholanate 5beta-cholanic acid-3alpha-ol CHEBI lithocholic acid Non-denaturing ionic detergent used for extraction of membrane proteins. A bile acid that is 5beta-cholan-24-oic acid bearing three alpha-hydroxy substituents at position 3, 7 and 12. CHOLIC ACID Cholic acid 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-oic acid 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanic acid Cholsaeure 3alpha,7alpha,12alpha-trihydroxy-5beta-cholanic acid (3alpha,5beta,7alpha,12alpha)-3,7,12-trihydroxycholan-24-oic acid C24H40O5 3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanate CHEBI cholic acid A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food. CARBON DIOXIDE dioxidocarbon carbon dioxide Carbon dioxide CO2 E-290 E290 E 290 dioxomethane carbonic anhydride O=C=O R-744 CHEBI carbon dioxide Any member of the class of organooxygen compounds that is a polyhydroxy-aldehyde or -ketone or a lactol resulting from their intramolecular condensation (monosaccharides); substances derived from these by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom; and polymeric products arising by intermolecular acetal formation between two or more such molecules (disaccharides, polysaccharides and oligosaccharides). Carbohydrates contain only carbon, hydrogen and oxygen atoms; prior to any oxidation or reduction, most have the empirical formula Cm(H2O)n. Compounds obtained from carbohydrates by substitution, etc., are known as carbohydrate derivatives and may contain other elements. Cyclitols are generally not regarded as carbohydrates. Kohlenhydrat glucido hydrates de carbone glucides carbohydrates Kohlenhydrate saccharidum glucidos carbohidratos saccharide carbohidrato saccharides glucide carbohydrate CHEBI carbohydrate chenodeoxycholic acid acts as an anionic detergents that often completely disrupt cell membranes and fully denature proteins. A dihydroxy-5beta-cholanic acid that is (5beta)-cholan-24-oic acid substituted by hydroxy groups at positions 3 and 7 respectively. 3alpha,7alpha-dihydroxy-5beta-cholan-24-oic acid Chenodeoxycholic acid Chenodiol gallodesoxycholic acid anthropodeoxycholic acid CDCA chenic acid 3alpha,7alpha-Dihydroxy-5beta-cholanic acid Chenix C24H40O4 anthropodesoxycholic acid 7alpha-hydroxylithocholic acid CHEBI chenodeoxycholic acid High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms. ChEBI deoxyribonucleic acid An aldohexose used as a source of energy and metabolic intermediate. glucose C6H12O6 Glc Glukose Glucose gluco-hexose CHEBI glucose The primary alcohol that is the simplest aliphatic alcohol, comprising a methyl and an alcohol group. Methylalkohol wood alcohol CH3OH Methyl alcohol wood naphtha carbinol MeOH wood spirit OXYMETHYLENE BRIDGING GROUP CH4O CO CHEBI methanol A secondary alcohol that is propane in which one of the hydrogens attached to the central carbon is substituted by a hydroxy group. i-propanol C3H8O Isopropanol 1-methylethyl alcohol IPA sec-propanol i-Propylalkohol Isopropyl alcohol 2-Propanol isopropyl alcohol CC(C)O Isopropylalkohol 2-hydroxypropane ISOPROPYL ALCOHOL 1-methylethanol CHEBI propan-2-ol A single-stranded RNA molecule containing about 70-90 nucleotides, folded by intrastrand base pairing into a characteristic secondary ('cloverleaf') structure that carries a specific amino acid and matches it to its corresponding codon on an mRNA during protein synthesis. tRNA; RNA, transfer CHEBI transfer RNA Sucrose is a disaccharide formed by glucose and fructose units joined by an acetal oxygen bridge from hemiacetal of glucose to the hemiketal of the fructose. Sucrose beta-D-fructofuranosyl alpha-D-glucopyranoside SUCROSE sacarosa beta-D-Fruf-(21)-alpha-D-Glcp Saccharose table sugar 1-alpha-D-Glucopyranosyl-2-beta-D-fructofuranoside Sacharose Cane sugar White sugar CHEBI sucrose RNA molecules which are essential structural and functional components of ribosomes, the subcellular units responsible for protein synthesis. rRNA CHEBI ribosomal RNA CHEBI hydroxy-5beta-cholanic acid inorganic sulfate salts inorganic sulfates CHEBI inorganic sulfate salt Any ribonucleic acid that is transfer RNA in which one or more of the free OH groups carries an alpha-aminoacyl group. Aminoacyl-tRNA CHEBI alpha-aminoacyl-tRNA An inorganic chloride salt having sodium(1+) as the counterion. Natriumchlorid halite [Na+].[Cl-] common salt Kochsalz NaCl ClNa salt cloruro sodico rock salt chlorure de sodium natrii chloridum table salt CHEBI sodium chloride digitonin acts as a nonionic detergent used to solubilize receptors and permeabilize cellular and nuclear membranes. A spirostanyl glycoside that has formula C56H92O29. Digitin digitin Digitonin CHEBI digitonin A dihydroxy-5beta-cholanic acid that has formula C24H40O4. Deoxycholic acid 3alpha,12alpha-dihydroxy-5beta-cholan-24-oic acid (3alpha,5alpha,8alpha,12alpha,14beta,17alpha)-3,12-dihydroxycholan-24-oic acid desoxycholic acid Desoxycholsaeure C24H40O4 7alpha-deoxycholic acid (3alpha,5beta,12alpha)-3,12-dihydroxycholan-24-oic acid (3ALPHA,5ALPHA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID 3alpha,12alpha-Dihydroxy-5beta-cholanic acid CHEBI deoxycholic acid A compound in which a hydroxy group, -OH, is attached to a saturated carbon atom. O[*] an alcohol HOR CHEBI alcohol In molecular biology, potassium acetate is used to precipitate dodecyl sulfate (DS) and DS-bound proteins, allowing the removal of proteins from DNA. It is also used as a salt for the ethanol precipitation of DNA. A potassium salt that has formula C2H3O2.K. Potassium acetate Potassium Acetate CHEBI potassium acetate potassium chloride (KCl) is a inorganic chloride composed of potassium and chloride. ClK potassium chloride sylvite KCl Kaon-Cl 10 Kaliumchlorid muriate of potash [KCl] Klotrix Klor-con Monopotassium chloride https://en.wikipedia.org/wiki/Potassium_chloride CHEBI potassium chloride An organic sodium salt that has formula C2H3NaO2. sodium acetate anhydrous C2H3NaO2 anhydrous sodium acetate acetic acid, sodium salt [Na+].CC([O-])=O Natriumazetat CHEBI sodium acetate organic aromatic compounds CHEBI organic aromatic compound ChEBI information biomacromolecule A macromolecule made up of nucleotide units and hydrolysable into certain pyrimidine or purine bases (usually adenine, cytosine, guanine, thymine, uracil), D-ribose or 2-deoxy-D-ribose and phosphoric acid. ChEBI nucleic acid High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins. ChEBI ribonucleic acid An RNA molecule that transfers the coding information for protein synthesis from the chromosomes to the ribosomes mRNA is formed from a DNA template by transcription. It may be a copy of a single gene or of several adjacent genes (polycistronic mRNA). On the ribosome, the sequence is converted into the programmed amino acid sequence through translation. template RNA; mRNA CHEBI messenger RNA Organic aromatic compounds having one or more hydroxy groups attached to a benzene or other arene ring. aryl alcohol arenols Aryl alcohol CHEBI phenols A substance used in a chemical reaction to detect, measure, examine, or produce other substances. chemical compound ChEBI reagent A hexose with a (potential) aldehyde group at one end. aldohexoses Aldohexose OCC(O)C(O)C(O)C(O)C=O aldohexose C6H12O6 CHEBI aldohexose A one-carbon compound that is methane in which three of the hydrogens are replaced by chlorines. trichloromethane CHCl3 Trichlormethan chloroforme [H]C(Cl)(Cl)Cl 1,1,1-trichloromethane chloroformium pro narcosi CHEBI chloroform Parent monosaccharides are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H-[CHOH]n-C(=O)[CHOH]m-H with three or more carbon atoms. The generic term 'monosaccharide' (as opposed to oligosaccharide or polysaccharide) denotes a single unit, without glycosidic connection to other such units. It includes aldoses, dialdoses, aldoketoses, ketoses and diketoses, as well as deoxy sugars, provided that the parent compound has a (potential) carbonyl group. Monosaccharid Monosacharid monosaccharides monosacarido monosacaridos Monosaccharide monosaccharide CHEBI monosaccharide cetyltrimethylammonium bromide acts a cationic detergent and is suitable for use in DNA precipitation. CTAB has been used for the isolation of plant high molecular weight DNA as well as plant DNA for use in PCR analysis. It has been utilized to precipitate nucleic acids. The organic bromide salt that is the bromide salt of cetyltrimethylammonium; one of the components of the topical antiseptic cetrimide. Cetyltrimethylammonium bromide N,N,N-trimethylhexadecan-1-aminium bromide N-Hexadecyl-N,N,N-trimethylammonium bromide Cetyl trimethyl ammonium bromide Bromuro de cetrimonio n-Hexadecyltrimethylammonium bromide N,N,N-Trimethylcetylammonium bromide Cetrimide Trimethylhexadecylammonium bromide N-Hexadecyltrimethylammonium bromide Bromat Cee dee Hexadecyl-trimethyl-ammonium bromide N-Cetyltrimethylammonium bromide Cetrimonium bromide Ctmab hexadecyltrimethylammonium bromide N,N,N-Trimethyl-1-hexadecanaminium bromide C19H42BrN CTAB Palmityltrimethyl ammonium bromide C19H42N.Br Cetrimonii bromidum Bromure de cetrimonium cetrimide CHEBI cetyltrimethylammonium bromide A secondary alcohol is a compound in which a hydroxy group, -OH, is attached to a saturated carbon atom which has two other carbon atoms attached to it. secondary alcohols CH2OR2 a secondary alcohol CHEBI secondary alcohol cholanoids bile acids and derivatives cholanoid A biological macromolecule minimally consisting of one polypeptide chain synthesized at the ribosome. ChEBI protein inorganic chloride salts inorganic chlorides inorganic chloride salt CHEBI inorganic chloride cholan-24-oic acids CHEBI cholanic acids organic sodium salts CHEBI organic sodium salt 2-Mercaptoethanol is used for reducing some proteins. 2-Mercaptoethanol is used in some RNA isolation procedures to eliminate ribonuclease released during cell lysis. Mercaptoethanol is an alkanethiol that has formula C2H6OS. Mercaptoethanol 2-sulfanylethanol Thioglycol beta-mercaptoethanol BETA-MERCAPTOETHANOL 2-Mercaptoethanol 2-mercaptoethanol 2-mercapto-ethanol 2-Mercapto-ethanol 2-Mercapto-Ethanol OCCS β-mercaptoethanol BME 2BME 2-ME β-met b-mercaptoethanol b-Mercaptoethanol CHEBI mercaptoethanol CHEBI double-stranded DNA ammonium salts Ammoniumsalze Ammoniumsalz CHEBI ammonium salt A metal chloride salt with a Li(+) counterion. LiCl [Li+].[Cl-] ClLi lithii chloridum cloruro de litio Lithiumchlorid chlorure de lithium CHEBI lithium chloride A compound in which monosaccharide units are joined by glycosidic linkages. The term is commonly used to refer to a defined structure as opposed to a polymer of unspecified length or a homologous mixture. When the linkages are of other types the compounds are regarded as oligosaccharide analogues. oligosacarido an oligosaccharide O-glycosylglycosides O-glycosylglycoside Oligosaccharide oligosaccharides oligosacaridos CHEBI oligosaccharide A polymer composed of PEG-ylated sorbitan [2-(1,2-dihydroxyethyl)tetrahydrofuran-3,4-diol] normally containing a total of 20 oxyethylene groups, with one or more of the terminal hydroxy groups esterified with a fatty acyl group. They are used as emulsifiers and dispersing agents in some pharmaceuticals products and as defoamers and emulsifiers in some foods. polysorbates CHEBI polysorbate Tween 40 acts as a non-ionic detergent used for cell lysis, nuclei isolation and cell fractionation. A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a palmitoyl group. polisorbato Tween 40 C62H122O26 Polysorbate 40 Polyoxyethylene (20) sorbitan monopalmitate polysorbate polysorbatum CHEBI polysorbate 40 TWEEN 20 acts as a non-ionic detergent. TWEEN 20 has been used in pre-extraction of membranes to remove peripheral proteins (used at 2% for extraction of membrane-bound proteins). TWEEN 20 has been used as a blocking agent for membrane based immunoassays at a typical concentration of 0.05%. TWEEN 20 can be used for lysing mammalian cells at a concentration of 0.005 to 0.5%. A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a dodecanoyl group. polysorbate Polysorbate 20 polysorbatum Polysorbate polisorbato C58H114O26 Tween 20 Polyoxyethylene sorbitan monolaurate Polyoxyethylene (20) sorbitan monolaurate CHEBI example of usage source: http://www.sigmaaldrich.com/catalog/product/sial/p1379?lang=en&region=CO&gclid=CjwKEAjw-vewBRDH1-b52Lig1hkSJACTPfVFKmIFgDeASxRzyjDXAt8-HmEYpgjOYCfQWDgPWdodbhoCRV3w_wcB polysorbate 20 Polyethylene glycol sorbitan monostearate, or TWEEN 60, has been used in a study to assess encapsulation of functional lipophilic components in surfactant-based colloidal delivery systems. It has also been used in a study to investigate doxorubicin loaded magneto-niosomes for targeted drug delivery. A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by a stearate group. Tween 60 polyoxyethylene (20) sorbitan monostearate Polyoxyethylene sorbitan monostearate Polysorbate 60 Polysorbate PEG-60 Sorbitan stearate C64H124O26 polysorbate polisorbato polysorbatum CHEBI example of usage source: http://www.sigmaaldrich.com/catalog/product/sigma/p1629?lang=en&region=CO polysorbate 60 Non-ionic detergent used for selective protein extraction and isolation of nuclei from mammalian cell lines. A polymer composed of PEG-ylated sorbitan, where the total number of poly(ethylene glycol) units is 20 (w + x + y + z = 20) and a single terminal is capped by an oleoyl group. Polysorbate 80 Tween 80 polysorbate Polyoxyethylene (20) sorbitan monooleate polisorbato Glycol (polysorbate 80) polysorbatum Polyethylene oxide sorbitan mono-oleate Polyoxyethylene sorbitan oleate C64H124O26 Polysorbate 80 Polyoxyethylene sorbitan monooleate CHEBI polysorbate 80 Pluronic acts as a non-ionic detergent, protects cells from hydrodynamic damage. A triblock copolymer composed of a central hydrophobic chain of poly(propylene oxide) flanked by two hydrophilic chains of poly(ethylene oxide). poloxamers poloxamer pluronics PEO-block-PPO-block-PEO PEO-b-PPO-b-PEO CHEBI pluronic A triblock copolymer composed of a central hydrophobic chain of poly(propylene oxide) (70 units) flanked by two hydrophilic chains of poly(ethylene oxide) (20 units each). A polymer with the formula HO[CH2CH2O]2O[CH2CH(CH3)O]70[CH2CH2O]2OH. Polyoxypropylene-polyoxyethylene block copolymer Poloxamer Block polyethylene-polypropylene glycol Block polyoxyethylene-polyoxypropylene Pluronic P123 Propylene oxide ethylene oxide block polymer Ethylene glycol-propylene glycol block copolymer CHEBI pluronic P-123 A polymer consisting of nonylbenzene with a poly(ethylene glycol) moiety attached at position 4. alpha-(4-nonylphenyl)-omega-hydroxypoly(oxyethylene) CHEBI tergitol An inorganic sulfate salt obtained by reaction of sulfuric acid with two equivalents of ammonia. A high-melting (decomposes above 280degreeC) white solid which is very soluble in water (70.6 g/100 g water at 0degreeC; 103.8 g/100 g water at 100degreeC), it is widely used as a fertilizer for alkaline soils. ammonium sulphate sulfuric acid, diammonium salt ammonium sulfate (2:1) [NH4+].[NH4+].[O-]S([O-])(=O)=O sulfuric acid ammonium salt (1:2) mascagnite (NH4)2SO4 H8N2O4S diammonium sulfate CHEBI ammonium sulfate [NH4+].CC([O-])=O E264 acetic acid, ammonium salt INS No. 264 C2H7NO2 CH3CO2NH4 ammonium ethanoate azanium acetate NH4OAc CH3COONH4 AcONH4 E-264 E 264 ammonium acetate Tergitol type NP-40 acts as a non-ionic detergent used for solubilizing proteins while maintaining native subunit structure, enzymatic activity, or other structural functions. Poly(ether) macoromolecule comprising a branched nonyl group bonded to one of the ring positions in 2-[phenoxypoly(ethoxy)]ethanol. A commericially available detergent, it is used to help crystallise proteins and extract the cytoplasmic contents of cellular culture. C9H13O2 Polyethylene glycol mono(branched p-nonylphenyl) ether branched alpha-(4-nonylphenyl)-omega-hydroxypoly(oxy-1,2-ethanediyl) Tergitol-type NP-40 Nonylphenol Ethoxylate NP40 Tergitol NP40 CHEBI nonyl phenoxypolyethoxylethanol An organic molecular entity containing a single carbon atom (C1). one-carbon compounds CHEBI one-carbon compound decyl beta-D-maltopyranoside acts as a non-ionic detergent used for solubilizing proteins while maintaining native subunit structure, enzymatic activity, or other structural functions. A glycoside resulting from attachment of a decyl group to the reducing-end anomeric centre of a beta-maltose molecule. Decyl β-D-malto­pyranoside Decyl-β-D-maltoside CHEBI decyl beta-D-maltopyranoside A ribonucleic acid with two complementary strands, similar to the DNA found in all cells. double stranded ribonucleic acid; dsRNA CHEBI double-stranded RNA A class of small RNA molecules which are comprised of approximately 150 nucleotides and which are found within the nucleus of eukaryotic cells. snRNAs; U-RNA; small nuclear ribonucleic acids; U-RNAs; small nuclear RNAs; snRNA; small nuclear ribonucleic acid CHEBI small nuclear RNA Nonidet P-40 acts as a non-ionic detergent used for solubilizing proteins while maintaining native subunit structure, enzymatic activity, or other structural functions. A poly(ether) macromolecule that is polyethylene glycol in which one of the terminal hydroxy groups has been converted to the corresponding p-octylphenyl ether. A nonionic, non-denaturing detergent, it is used for solubilising membrane proteins during isolation of membrane-protein complexes. (C2H4O)nC14H22O Nonidet P40 polyethylene glycol mono(4-octylphenyl) ether octylphenolpoly(ethyleneglycolether) polyethylene glycol mono(octylphenyl) ether polyethylene glycol mono(p-octylphenyl) ether Nonylphenyl-polyethylene glycol CHEBI Nonidet P-40 A threonylcarbamoyladenosine that is incorporated into a tRNA molecule. CHEBI tRNA threonylcarbamoyladenosine Sodium dodecyl sulfate acts as a anionic detergent that often completely disrupt cell membranes and fully denature proteins. An alkyl sulfate that has formula C12H25NaO4S. sodium dodecylsulfate C12H25O4S.Na C12H25NaO4S SDS sodium lauryl sulphate sodium dodecyl sulphate SLS Sodium lauryl sulfate CHEBI sodium dodecyl sulfate CHEBI single-stranded DNA Sodium deoxycholate acts as a anionic detergent; useful for extraction of membrane receptors and other plasma membrane proteins and for nuclei isolation. A bile acid salt that has formula C24H39NaO4. sodium 7-deoxycholate C24H39NaO4 desoxycholate sodium sodium desoxycholate deoxycholic acid sodium salt deoxycholate sodium Sodium deoxycholate C24H39O4.Na sodium deoxycholate sodium 3alpha,12alpha-dihydroxy-5beta-cholan-24-oate CHEBI example of usage source: http://www.sigmaaldrich.com/catalog/product/sial/d6750?lang=en&region=CO sodium deoxycholate Triton X-100 acts as a nonionic surfactant used for solubilizing proteins while maintaining native subunit structure, enzymatic activity, or other structural functions. Triton X-100 is a A poly ethylene glycol terminated with a 4-(2,4,4-trimethylpentan-3-yl) phenyl group at one end. Poly(oxyethylene)-p-tert-octylphenyl ether Polyethylene glycol mono(p-(1,1,3,3-tetramethylbutyl)phenyl) ether octoxinolum Peg (p-(1,1,3,3-tetramethylbutyl)phenyl) ether Peg 4-isooctylphenyl ether Polyoxyethylene mono(octylphenyl) ether alpha-(4-(1,1,3,3-Tetramethylbutyl)phenyl)-omega-hydroxypoly(oxy-1,2-ethanediyl) (C2H4O)nC14H22O 4-tert-Octylphenyl peg ether Polyethylene glycol mono(p-tert-octylphenyl) ether Peg 4-tert-octylphenyl ether Polyoxyethylene 4-(1,1,3,3-tetramethylbutyl)phenyl ether 4-(1,1,3,3-Tetramethylbutyl)phenyl hydroxypoly(oxyethylene) octoxinol Octoxynol 9 Triton X - 100 triton X-100 triton X - 100 triton x-100 triton x - 100 Triton-X 100 triton-X 100 CHEBI Triton X-100 a immortal cell line that is dervied from human tissue. immortal human cell line cell line ontology (CLO) immortal human cell line cell a immortal contractile cell line cell that is derived from muscle cell cell line ontology (CLO) immortal muscle cell line cell a immortal electrically responsive cell line cell that is derived from neuron. cell line ontology (CLO) immortal neuron cell line cell a immortal neuron cell line cell that is derived from peripheral neuron cell line ontology (CLO) immortal peripheral neuron cell line cell immortal animal cell line cell line ontology (CLO) immortal animal cell line cell a immortal animal cell line that is derived from epithelial cell cell line ontology (CLO) immortal epithelial cell line cell a immortal animal cell line that is derived from neural cell immortal neural cell line cell line ontology (CLO) immortal neural cell line cell a immortal epithelial cell line cell that is derived from HeLa cell cell line ontology (CLO) HeLa cell derived cell line cell An immortal cell line cell that derives from prostate gland. cell line ontology (CLO) immortal prostate gland-derived cell line cell An immortal cell line cell that derives from liver. cell line ontology (CLO) immortal liver-derived cell line cell An immortal cell line cell that derives from colon. cell line ontology (CLO) immortal colon-derived cell line cell An immortal cell line cell that derives from neural nucleus. cell line ontology (CLO) immortal neural nucleus-derived cell line cell An immortal epithelial cell line cell that derives from uterine cervix. cell line ontology (CLO) immortal uterine cervix-derived epithelial cell line cell An immortal colon-derived cell line cell that derives from human. cell line ontology (CLO) immortal human colon-derived cell line cell An immortal peripheral neuron cell line cell that derives from human. cell line ontology (CLO) immortal human peripheral neuron cell line cell An immortal liver-derived cell line cell that derives from human. cell line ontology (CLO) immortal human liver-derived cell line cell An immortal neural nucleus-derived cell line cell that derives from rat. cell line ontology (CLO) immortal rat neural nucleus-derived cell line cell An immortal uterine cervix-derived epithelial cell line cell that derives from human. cell line ontology (CLO) immortal human uterine cervix-derived epithelial cell line cell An immortal prostate gland-derived cell line cell that derives from human. cell line ontology (CLO) immortal human prostate gland-derived cell line cell A431 cell line ontology (CLO) A431 cell C6 cell line ontology (CLO) disease: glial tumor C6 cell HCT 116 HCT116 HCT-116 cell line ontology (CLO) HCT 116 cell HeLa cell line ontology (CLO) HeLa cell Hep G2 Hep-G2 HEPG2 HEP-G2 cell line ontology (CLO) disease: hepatocellular carcinoma Hep G2 cell JURKAT jurkat cell line ontology (CLO) disease: leukemia, T cell JURKAT jurkat JURKAT cell LNCaP LNCAP cell line ontology (CLO) LNCAP LNCaP LNCAP cell A immortal human cell line cell that has the characteristics: Lung carcinoma, refer to ATCC CCL185 RCB0098 A549 cell line ontology (CLO) RCB0098 cell A immortal mouse muscle cell line cell that has the characteristics: Said differentiate to myotubes, but need confirmation. C2C12 RCB0987 c2C12 cell line ontology (CLO) RCB0987 cell A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. cell type ontology (CL) The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). cell A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped. cell type ontology (CL) These cells may be vimentin-positive, fibronectin-positive, fsp1-positive, MMP-1-positive, collagen I-positive, collagen III-positive, and alpha-SMA-negative. fibroblast cell type ontology (CL) fungal cell cell type ontology (CL) primary neuron The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system. nerve cell cell type ontology (CL) These cells are also reportedly CD4-negative and CD200-positive. They are also capable of producing CD40L and IFN-gamma. neuron cell type ontology (CL) animal cell A cell that is part of the nervous system. cell type ontology (CL) neural cell Microsoft Word is commonly used word processing software. Software is a general term primarily used for digitally stored data such as computer programs and other kinds of information read and written by computers. http://en.wikipedia.org/wiki/Computer_software ERO software A primer Reagent that is a polymer comprised of nucleotides, each of which consists of three components: a nitrogenous heterocyclic base, which is either a purine or a pyrimidine; a pentose sugar; and a phosphate group. http://en.wikipedia.org/wiki/Nucleic_acid ERO nucleic acid reagent A primer. A reagent that is a polymer comprised of DNA nucleotides. PERSON: Matthew Brush ERO DNA reagent A primer. A DNA reagent consisting of a short, linear DNA polymer, typically with 100 or fewer bases. DNA oligo ERO DNA oligonucleotide An information content entity that is a mark or character used as a conventional representation of another entity. IAO symbol Examples of information content entites include journal articles, data, graphical layouts, and graphs. an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity OBI_0000142 OBI information content entity Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. group:OBI OBI_0000042 OBI data set A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. IAO version number Words, sentences, paragraphs, and the written (non-figure) parts of publications are all textual entities A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. text OBI textual entity A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole OBI document An abstract, introduction, method or results section. an information content entity that is part of a document OBI document part Lawrence Hunter and Kevin Brettonel Cohen part of a document that enumerates the authors of the document IAO author list Mus (commonly mice) is a small mammal belonging to the order of rodents. mice mouse NCBITaxon Mus mouse Mus muscaris house mouse mice C57BL/6xCBA/CaJ hybrid NCBITaxon Mus musculus Trypanosoma (Trypanozoon) brucei brucei T. b. brucei NCBITaxon Trypanosoma brucei brucei Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells a device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled http://www.medterms.com/script/main/art.asp?articlekey=18426 OBI incubator a material obtained from an organism in order to be a representative of the whole sample specimen biospecimen OBI sample from organism blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general. A material entity that has the material sample role sample population OBI material sample Amplied DNA created by PCR DNA that has been produced in an enzymatic amplification process Alan Ruttenberg OBI amplified DNA The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas. Group: UPenn group OBI DNA extract A device that is used to freeze dry material. http://en.wikipedia.org/wiki/Freeze_drying OBI lyophilizer A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint. http://en.wikipedia.org/wiki/Laboratory_centrifuge OBI microcentrifuge A microinjection device that is used to measure very small volumes of liquids. http://www.answers.com/topic/micropipette OBI micropipette A symbol denotes a specimen and used to distinguish one specimen from another in an investigation. sample identifier OBI specimen identifier fungus, animal, virus, plant A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. http://en.wikipedia.org/wiki/Organism OBI organism A device with a rapidly rotating container that applies centrifugal force to its contents http://en.wikipedia.org/wiki/Centrifuge OBI centrifuge Sonicator 3000 A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions. OBI sonicator Piko(tm) 96-well Thermal Cycler An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. DNA_amplifier PCR_machine Polymerase_Chain_Reaction_ machine thermocycler MO OBI thermal cycler VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 degrees C. An oil bath is employed for temperatures over 100 degrees C. A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well. OBI Instrument branch OBI temperature control bath A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours. A water bath is a temperature control bath in which a water acts as contact medium enabling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure). OBI water bath A plant cell that is grown or maintained in vitro. cell suspension cultured cell plant tissue culture plant ontology (PO) Includes isolated plant cells and small plant cell aggregates that proliferate while suspended in sterile liquid medium or spread on a solid agar medium. cultured plant cell A cultured plant cell from which the entire plant cell wall has been removed. protoplast plant ontology (PO) The cell wall is generally removed using polysaccharide-degrading enzymes such as cellulase, pectinase and /or xylanase. The cultured plant cell may be in suspension culture or from callus culture on solid media. plant protoplast A cultured plant cell that was derived from leaf tissue. plant ontology (PO) May be derived from cultured plant callus or plant protoplast that was induced from a segment of leaf. In the case of the plant protoplast, after the re-establishment cell walls. leaf-derived cultured plant cell A cultured plant cell that was derived from root tissue. plant ontology (PO) May be derived from cultured plant callus or plant protoplasts induced from a segment of root. In the case of the plant protoplast, after the re-establishment plant cell walls. root-derived cultured plant cel A cell which is a plant structure (PO:0009011). plant ontology (PO) Applies to cells that are living or dead at maturity (e.g., fiber cell or tracheid) and includes any external encapsulating structures (if present) such as the plasma membrane and the plant-type cell wall. Definition of cell GO:0005623: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope". GO:0009505. Definition of plant-type cell wall (GO:0009505): A more or less rigid structure lying outside the cell membrane of a cell and composed of cellulose and pectin and other organic and inorganic substances, synonym; exact: cellulose and pectin-containing cell wall. plant cell roots, leaves, flowers, stems. A plant structure (PO:0009011) that consists predominantly of similarly specialized plant cells (PO:0009002) of one or more types. portion of plant tissue portion of tissue plant ontology (PO) plant tissue A multi-tissue plant structure (PO:0025496) that develops from a plant ovule (PO:0020003) and has as parts a plant embryo (PO:0009009) enclosed in a seed coat (PO:0009088). pyrene diaspore semilla seed tissue plant ontology (PO) A seed generally develops from an ovule (PO:0020003) after fertilization, but may develop without fertilization in the case of apogamy (e.g., adventitious embryos or somatic embryos). A seed is a reproductive unit of seed plants (gymnosperms, angiosperms, and fossil pteridosperms). seed A determinate reproductive shoot system that has as part at least one carpel or at least one stamen and does not contain any other determinate shoot system as a part. diclinous flower pistillate flower staminate flower basal flower double flower female flower hermaphrodite flower male flower perfect flower imperfect flower monoclinous flower flor plant ontology (PO) flower A shoot axis (PO:0025029) that is the primary axis of a plant. stalk trunk cane caudices primocane scape caudex bole primary stem tallo tronco culm; eje primario primary axis plant ontology (PO) Often bears leaves and buds. It is usually above ground, more or less negatively geotropic, and exogenous in origin. stem A collective plant organ structure (PO:0025007) that produces root apical meristems (PO:0020147) and the plant structures that arise from them. root tissue plant ontology (PO) root A phyllome (PO:0006001) that is not associated with a reproductive structure. hoja leaf sample leaves leaf tissue leaf material fresh-leaf tissue fresh leaf tissue dried leaf tissue dried leaf sample dried leaf Leaf blade plant ontology (PO) leaf Any portion of plant tissue (PO:0009007) other than epidermis (PO:0005679) or vascular tissue (PO:0009015). portion of ground tissue plant ontology (PO) ground tissue portion of ground tissue a DNA moelcule representing sequence reverse transcribed from a messenger RNA template, in a reaction catalyzed by the enzyme reverse transcriptase and the enzyme DNA polymerase. cDNA REO complementary DNA a nucleoside triphosphate reagent containing three phosphate groups bound to a 2'-deoxyribo- sugar ring dNTP reagent dNTPs dNTP mix Deoxynucleoside triphosphates deoxynucleoside triphosphates Deoxynucleotide triphosphates deoxynucleotide triphosphates Deoxynucleotide (dNTP) Solution Set Deoxynucleotide (dNTP) Solution Mix REO deoxyribonucleoside triphosphate reagent A nucleoside triphosphate reagent is a reagent that is a nucleoside containing three phosphate groups bound to its sugar ring. NTP reagent REO nucleoside triphosphate reagent A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ. chambered heart vertebrate heart Herz branchial heart Entire heart UBERON heart The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. UBERON brain Respiration organ that develops as an oupocketing of the esophagus. pulmo UBERON Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung the organ that functions to filter blood and to store red corpuscles and platelets lien UBERON spleen An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. jecur iecur UBERON liver A paired organ of the urinary tract which has the production of urine as its primary function. reniculate kidney UBERON kidney a human being that bears an author role. Ontology for genetic interval author AMV reverse transcriptase is an enzyme from the avian myeloblastosis virus like HIV has two subunits, a 63kDa subunit and a 95kDa subunit. Avian Myeloblastosis Virus (AMV) Reverse Transcriptase Avian Myeloblastosis Virus Reverse Transcriptase Reverse Transcriptase AMV AMV RT http://link.springer.com/article/10.1007%2Fs10529-012-0904-9 AMV reverse transcriptase is an enzyme from the avian myeloblastosis virus like HIV has two subunits, a 63kDa subunit and a 95kDa subunit. Definition source: http://link.springer.com/article/10.1007%2Fs10529-012-0904-9 AMV reverse transcriptase Avian Myeloblastosis Virus (AMV) Reverse Transcriptase Avian Myeloblastosis Virus Reverse Transcriptase Reverse Transcriptase AMV AMV RT Advantage 2 PCR buffer is a buffer optimized for amplifying genomic DNA, and in particular with products less than 1-2 kb. Advantage 2 PCR Buffer 10X Advantage 2 SA PCR Buffer Advantage 2 SA PCR Buffer file:///Users/olgaxgiraldop/Downloads/PT3281-1_PR9Z3414%20(1).pdf Advantage 2 PCR buffer is a buffer optimized for amplifying genomic DNA, and in particular with products less than 1-2 kb. Definition source: file:///Users/olgaxgiraldop/Downloads/PT3281-1_PR9Z3414%20(1).pdf Advantage 2 PCR buffer Advantage 2 PCR Buffer 10X Advantage 2 SA PCR Buffer Advantage 2 SA PCR Buffer Advantage of the protocol is a subclass of textual entity. It should be made clear in which situations the Protocol has been successfully employed. http://www.nature.com/nprot/info/gta.html Advantage of the protocol is a subclass of textual entity. It should be made clear in which situations the Protocol has been successfully employed. Definition source: http://www.nature.com/nprot/info/gta.html advantage of the Protocol Agarose Gel Electrophoresis Protocol is a subclass of laboratory protocol. Agarose Gel Electrophoresis Protocol is a step by step description of a procedure used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. Agarose Gel Electrophoresis Protocol is a subclass of laboratory protocol. Agarose Gel Electrophoresis Protocol is a step by step description of a procedure used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field. agarose gel electrophoresis protocol alkali metal salts usually are very water soluble. Some alkali metal salt are: potasium salt, sodium salt. alkali metal salt reagent an alkanesulfonate O3RS alkanesulfonates alkanesulfonate reagent an alkanesulfonate O3RS alkanesulfonates A sodium dodecyl sulfate. Alkyl sulfate reagent is a reagent commonly used as an anionic surfactant in liquid soaps, detergents to clean wool, surface cleaners, as active ingredients in laundry detergents, shampoos and conditioners. HO4SR alkyl sulfates https://en.wikipedia.org/wiki/Organosulfate Alkyl sulfate reagent is a reagent commonly used as an anionic surfactant in liquid soaps, detergents to clean wool, surface cleaners, as active ingredients in laundry detergents, shampoos and conditioners. Definition source: https://en.wikipedia.org/wiki/Organosulfate Example of usage: A sodium dodecyl sulfate. alkyl sulfate reagent HO4SR alkyl sulfates AmpliTaq DNA Polymerase is a 94 kDa, thermostable, recombinant DNA polymerase obtained by expression of a modified form of the Thermus aquaticus (Taq) DNA polymerase gene in E. coli. https://www.thermofisher.com/order/catalog/product/N8080155 AmpliTaq DNA Polymerase is a 94 kDa, thermostable, recombinant DNA polymerase obtained by expression of a modified form of the Thermus aquaticus (Taq) DNA polymerase gene in E. coli. Definition source: https://www.thermofisher.com/order/catalog/product/N8080155 AmpliTaq DNA Polymerase AmpliTaq Gold is a thermostable DNA polymerase designed to make advanced polymerase Chain Reaction techniques. The key component in AmpliTaq Gold is AmpliTaq® DNA Polymerase (Deoxynucleoside triphosphate: DNA Deoxynucleotidyltransferase, E.C.2.7.7.7). AmpliTaq Gold DNA Polymerase http://mvz.berkeley.edu/egl/inserts/AmpliTaq%20Gold_041554.pdf AmpliTaq Gold is a thermostable DNA polymerase designed to make advanced polymerase Chain Reaction techniques. The key component in AmpliTaq Gold is AmpliTaq® DNA Polymerase (Deoxynucleoside triphosphate: DNA Deoxynucleotidyltransferase, E.C.2.7.7.7). Definition source: http://mvz.berkeley.edu/egl/inserts/AmpliTaq%20Gold_041554.pdf AmpliTaq Gold AmpliTaq Gold DNA Polymerase DNA recovered from ancient biological material (e.g., archaeological and historical skeletal material, mummified tissues, preserved plant remains, ice and permafrost cores). NCI Thesaurus Ancient DNA ancient DNA A animal euthanization protocol is a protocol used in a parasitology experiments and defines instructions on how end the life of animals. A animal euthanization protocol is a protocol used in a parasitology experiments and defines instructions on how end the life of animals. animal euthanization protocol Apex Taq DNA Polymerase is a thermostable enzyme. The enzyme is isolated from Thermus aquaticus and has a molecular weight of approximately 94 kDa. APEX Taq polymerase APEX taq DNA polymerase Apex taq DNA polymerase https://corebio.ucsd.edu/4DCGI/Catalog/ProductDetail.html?prod_id=7924 Apex Taq DNA Polymerase is a thermostable enzyme. The enzyme is isolated from Thermus aquaticus and has a molecular weight of approximately 94 kDa. Definition source: https://corebio.ucsd.edu/4DCGI/Catalog/ProductDetail.html?prod_id=7924 Apex Taq DNA Polymerase APEX Taq polymerase APEX taq DNA polymerase Apex taq DNA polymerase The protocol works in northern blot assays using cactus, agave, banana, tomato, Arabidopsis and tobacco. Allwood, J.W., et al., Inter-laboratory reproducibility of fast gas chromatography-electron impact-time of flight mass spectrometry (GC-EI-TOF/MS) based plant metabolomics. Metabolomics, 2009. 5(4): p. 479-496. Application of the protocol is a subclass of textual entity. Applications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol. Application of the protocol is a subclass of textual entity. Applications of the protocol list the full diversity of the applications of the method and support if is possible to extend the range of applications of the protocol. Example of usage: The protocol works in northern blot assays using cactus, agave, banana, tomato, Arabidopsis and tobacco. Allwood, J.W., et al., Inter-laboratory reproducibility of fast gas chromatography-electron impact-time of flight mass spectrometry (GC-EI-TOF/MS) based plant metabolomics. Metabolomics, 2009. 5(4): p. 479-496. application of the protocol Any ether in which the oxygen is attached to at least one aryl substituent. aromatic ethers CHEBI Any ether in which the oxygen is attached to at least one aryl substituent. Definition source: CHEBI aromatic ether reagent aromatic ethers orcid ID Author identifier is a unique number to all authors as a form of authority control. Author identifier is a unique number to all authors as a form of authority control. Example of usage: orcid ID author identifier Olga Giraldo Author name is a textual entity. Author name is the name of a person or institution. If is applicable, the author name should include the first name and last name. Author name is a textual entity. Author name is the name of a person or institution. If is applicable, the author name should include the first name and last name. Example of usage: Olga Giraldo author name Laboratory bags: autoclavable biohazard bags, specimen/document zipper bags A bag is a supply. A bag is a simple tool in the form of a non-rigid container. A bag is a supply. A bag is a simple tool in the form of a non-rigid container. Example of usage: Laboratory bags: autoclavable biohazard bags, specimen/document zipper bags bag Disruption caused by collision with agitated beads in liquid suspension. Disruption caused by collision with agitated beads in liquid suspension. bead beater Any member of a group of steroid carboxylic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. Bile acid Bile salt Gallensaeure bile acids Gallensaeuren Any member of a group of steroid carboxylic acids occuring in bile, where they are present as the sodium salts of their amides with glycine or taurine. bile acid reagent Bile acid Bile salt Gallensaeure bile acids Gallensaeuren A salt of a bile acid. CHEBI bile acid salt reagent blender is an instrument that ensure a homogenized blending of the diluted sample. blender is an instrument that ensure a homogenized blending of the diluted sample. blender DNA purification Buffer AL is a lysis buffer used during DNA isolation using QIAamp and DNeasy kits. Buffer AL AL buffer AL Buffer file:///Users/olgaxgiraldop/Downloads/HB12500021076579%20PS%20DNY%20Buffer%20AL%200513%20WW.pdf Buffer AL is a lysis buffer used during DNA isolation using QIAamp and DNeasy kits. Definition source: file:///Users/olgaxgiraldop/Downloads/HB12500021076579%20PS%20DNY%20Buffer%20AL%200513%20WW.pdf Example of usage: DNA purification buffer AL Buffer AL AL buffer AL Buffer DNA purification Buffer AP1 is a lysis buffer used during isolation of DNA from plant tissue with the DNeasy Plant Mini Kit. Buffer AP1 AP1 buffer AP1 Buffer http://www.calpoly.edu/~bio/ubl/protocols_files/qiaplant.pdf Buffer AP1 is a lysis buffer used during isolation of DNA from plant tissue with the DNeasy Plant Mini Kit. Definition source: http://www.calpoly.edu/~bio/ubl/protocols_files/qiaplant.pdf Example of usage: DNA purification buffer AP1 Buffer AP1 AP1 buffer AP1 Buffer buffer AP2 Buffer ATL is a lysis buffer for use in purification of nucleic acids. ATL buffer ATL Buffer Buffer ATL https://www.qiagen.com/es/shop/lab-essentials-and-accessories/buffer-atl/ Buffer ATL is a lysis buffer for use in purification of nucleic acids. Definition source: https://www.qiagen.com/es/shop/lab-essentials-and-accessories/buffer-atl/ buffer ATL ATL buffer ATL Buffer Buffer ATL Buffer B1 (Bacterial Lysis Buffer 1) consists of 50 mM Tris•Cl pH 8.0; 50 mM EDTA pH 8.0; 0.5% Tween 20; 0.5% Triton-X100. Buffer B1 is used in combination with lysozyme or lysostaphin and proteinase K for the efficient lysis of bacteria prior to DNA purification using QIAGEN Genomic-tips. Bacterial Lysis Buffer 1 https://www.qiagen.com/es/resources/faq?id=569abfa9-c05c-4a20-ae6b-793630da3d55&lang=en Buffer B1 (Bacterial Lysis Buffer 1) consists of 50 mM Tris•Cl pH 8.0; 50 mM EDTA pH 8.0; 0.5% Tween 20; 0.5% Triton-X100. Buffer B1 is used in combination with lysozyme or lysostaphin and proteinase K for the efficient lysis of bacteria prior to DNA purification using QIAGEN Genomic-tips. Definition source: https://www.qiagen.com/es/resources/faq?id=569abfa9-c05c-4a20-ae6b-793630da3d55&lang=en buffer B1 Bacterial Lysis Buffer 1 Buffer B2 (Bacterial Lysis Buffer 2) consists of 3 M guanidine hydrochloride, 20% Tween 20. Buffer B2 is used in combination with Buffer B1, lysozyme or lysostaphin and Proteinase K for efficient lysis of bacteria prior to DNA purification using QIAGEN Genomic-tips. Bacterial Lysis Buffer 2 https://www.qiagen.com/es/resources/faq?id=92b08ae8-b395-4961-b71b-b1e784c7c8ea&lang=en Buffer B2 (Bacterial Lysis Buffer 2) consists of 3 M guanidine hydrochloride, 20% Tween 20. Buffer B2 is used in combination with Buffer B1, lysozyme or lysostaphin and Proteinase K for efficient lysis of bacteria prior to DNA purification using QIAGEN Genomic-tips. Definition source: https://www.qiagen.com/es/resources/faq?id=92b08ae8-b395-4961-b71b-b1e784c7c8ea&lang=en buffer B2 Bacterial Lysis Buffer 2 cell lysis buffer cell lysis buffer buffer C1 1X Queen’s lysis buffer (1L), AB lysis buffer (500ml). Buffer name is a textual entity. Buffer name is the name of the buffer produced by or used in a reaction involving changes in atoms or molecules. If is applicable, the name of the buffer should be including the follow information: buffer concentration, and final volume. Buffer name is a textual entity. Buffer name is the name of the buffer produced by or used in a reaction involving changes in atoms or molecules. If is applicable, the name of the buffer should be including the follow information: buffer concentration, and final volume. Example of usage: 1X Queen’s lysis buffer (1L), AB lysis buffer (500ml). buffer name yeast lysis buffer yeast lysis buffer buffer Y1 DNA purification CTAB buffer is a buffer used during the extraction/isolation of highly polymerized DNA from plant material. The main chemical compound, CTAB, simultaneously solubilizes the plant cell wall and lipid membranes of internal organelles and denatures proteins (enzymes). CTAB extraction buffer CTAB DNA extraction buffer PERSON:Olga Giraldo CTAB buffer is a buffer used during the extraction/isolation of highly polymerized DNA from plant material. The main chemical compound, CTAB, simultaneously solubilizes the plant cell wall and lipid membranes of internal organelles and denatures proteins (enzymes). Example of usage: DNA purification CTAB buffer CTAB extraction buffer CTAB DNA extraction buffer 5000-0012 Catalog number is a subclass of textual entity. Catalog number is a numeral or string of numerals that is used for identification. Catalog number is a subclass of textual entity. Catalog number is a numeral or string of numerals that is used for identification. Example of usage: 5000-0012 catalog number Breaking the cells open, is the first basic step in a DNA extraction. This is commonly achieved by chemical and physical methods-blending, grinding or sonicating the sample. Cell lysis Breaking the cells open, is the first basic step in a DNA extraction. This is commonly achieved by chemical and physical methods-blending, grinding or sonicating the sample. cell disruption Cell lysis Weigh 300-400 mg of ground, lyophilized tissue, into a 15 ml polypropylene centrifuge tube. Centrifuge tube is a supply. centrifuge tubes are tapered tubes of various sizes made of glass or plastic. They may vary in capacity from tens of millilitres. centrifuge tips http://en.wikipedia.org/wiki/Laboratory_centrifuge#Centrifuge_tubes Centrifuge tube is a supply. centrifuge tubes are tapered tubes of various sizes made of glass or plastic. They may vary in capacity from tens of millilitres. Definition source: http://en.wikipedia.org/wiki/Laboratory_centrifuge#Centrifuge_tubes Example of usage: Weigh 300-400 mg of ground, lyophilized tissue, into a 15 ml polypropylene centrifuge tube centrifuge tube centrifuge tips chloride salts chlorides Chloride salts such as sodium chloride are often very soluble in water. It is an essential electrolyte located in all body fluids responsible for maintaining acid/base balance, transmitting nerve impulses and regulating fluid in and out of cells. chloride salt reagent chloride salts chlorides mixture suitable for nucleic acid purification in plants. mixture suitable for nucleic acid purification in plants. Chloroform:Isoamyl alcohol Coffee mill is an instrument used (during the first stage of nucleic acids purification), to crush leaf tissue to make leaf powder. coffee grinder Coffee mill is an instrument used (during the first stage of nucleic acids purification), to crush leaf tissue to make leaf powder. coffee mill coffee grinder A macromolecule derived from two or more species of monomer. copolymers co-polymers copolymer co-polymer heteropolymers heteropolymer CHEBI copolymer macromolecule reagent Remove the combs and flush out the wells using a syringe. This is a CRITICAL STEP, especially for polymorphic bands that are close to each other. Otherwise, unpolymerized acrylamide solution will be polymerized at the bottom of the wells and will affect the migration of the fragments. (Laboratory Protocols CIMMYT, 2005) CRITICAL STEP: The supernatant in each step should be carefully transferred without disturbing the other layers. (Sudha, 2012) A critical step is a message given to a user to perform a protocol instruction in a very precise manner e.g., where the time and temperature of a step is crucial or the use of RNase free solutions is required. A critical step is a message given to a user to perform a protocol instruction in a very precise manner e.g., where the time and temperature of a step is crucial or the use of RNase free solutions is required. Example of usage: Remove the combs and flush out the wells using a syringe. This is a CRITICAL STEP, especially for polymorphic bands that are close to each other. Otherwise, unpolymerized acrylamide solution will be polymerized at the bottom of the wells and will affect the migration of the fragments. (Laboratory Protocols CIMMYT, 2005) CRITICAL STEP: The supernatant in each step should be carefully transferred without disturbing the other layers. (Sudha, 2012) critical step An animal cell that is grown or maintained in vitro. cell suspension cultured cell animal tissue culture An animal cell that is grown or maintained in vitro. cultured animal cell cell suspension cultured cell animal tissue culture cultured mammalian cells cultured mammalian cell cultured mammalian cells The cytoplasmic extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. This buffer causes selective membrane permeabilization, releasing soluble cytoplasmic contents. CEB CEB buffer https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html The cytoplasmic extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. This buffer causes selective membrane permeabilization, releasing soluble cytoplasmic contents. Definition source: https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html cytoplasmic extraction buffer CEB CEB buffer DNA extraction protocol is a subclass of nucleic acid extraction protocol. DNA extraction protocol, is a step by step description of a procedure in which is recovered a fraction of DNA from a material entity. DNA isolation protocol DNA extraction protocol is a subclass of nucleic acid extraction protocol. DNA extraction protocol, is a step by step description of a procedure in which is recovered a fraction of DNA from a material entity. DNA extraction protocol DNA isolation protocol A material entity which results from the aggregation of DNA produced by the application of centrifugal force to a liquid containing DNA in suspension. Adapted from OBI A material entity which results from the aggregation of DNA produced by the application of centrifugal force to a liquid containing DNA in suspension. Definition source: Adapted from OBI DNA pellet DNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix. DNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix. DNA separated by molecular size The biological activity of a biopolymer is closely linked to its native structure which is retained only if critical factors such as temperature, pH, solvent and solute are kept within narrow limits. Any alteration of the native structure causing a loss of biological activity is called denaturation. http://www.sigmaaldrich.com/life-science/metabolomics/bioultra-reagents/denaturation.html#sthash.5rKMTmls.dpuf The biological activity of a biopolymer is closely linked to its native structure which is retained only if critical factors such as temperature, pH, solvent and solute are kept within narrow limits. Any alteration of the native structure causing a loss of biological activity is called denaturation. Definition source: http://www.sigmaaldrich.com/life-science/metabolomics/bioultra-reagents/denaturation.html#sthash.5rKMTmls.dpuf denaturation reaction A carbohydrate derivative that is formally obtained from a disaccharide. disaccharide derivatives CHEBI disaccharide derivative reagent A compound in which two monosaccharides are joined by a glycosidic bond. Disaccharide disaccharides Disaccharid disacarido disacaridos Disacharid CHEBI disaccharide reagent DTT is used as a reducing or "deprotecting" agent for thiolated DNA. DTT is frequently used to reduce the disulfide bonds of proteins. DTT can also be used as an oxidizing agent. Dithiothreitol (DTT) is the common name for a small-molecule redox reagent also known as Cleland's reagent. DTT's formula is C4H10O2S2. Its name derives from the four-carbon sugar, threose. DTT has an epimeric ('sister') compound, dithioerythritol (DTE). rel-(2R,3R)-1,4-disulfanylbutane-2,3-diol 1,4-Dithiothreitol 1,4-dithiothreitol Cleland's reagent rac-Dithiothreitol threo-1,4-Dimercapto-2,3-butanediol DTT (R*,R*)-1,4-dimercapto-2,3-butanediol Dithiothreitol Dithiotreitol C4H10O2S2 DL-threo-1,4-Dimercapto-2,3-butanediol DTL https://en.wikipedia.org/wiki/Dithiothreitol Dithiothreitol (DTT) is the common name for a small-molecule redox reagent also known as Cleland's reagent. DTT's formula is C4H10O2S2. Its name derives from the four-carbon sugar, threose. DTT has an epimeric ('sister') compound, dithioerythritol (DTE). Definition source: https://en.wikipedia.org/wiki/Dithiothreitol Example of usage: DTT is used as a reducing or "deprotecting" agent for thiolated DNA. DTT is frequently used to reduce the disulfide bonds of proteins. DTT can also be used as an oxidizing agent. dithiothreitol rel-(2R,3R)-1,4-disulfanylbutane-2,3-diol 1,4-Dithiothreitol 1,4-dithiothreitol Cleland's reagent rac-Dithiothreitol threo-1,4-Dimercapto-2,3-butanediol DTT (R*,R*)-1,4-dimercapto-2,3-butanediol Dithiothreitol Dithiotreitol C4H10O2S2 DL-threo-1,4-Dimercapto-2,3-butanediol DTL Shearing caused by a round glass pestle that is manually driven into a glass tube tissue grinder Shearing caused by a round glass pestle that is manually driven into a glass tube dounce homogenizer tissue grinder a tool or machine with a rotating cutting tip or reciprocating hammer or chisel, used for making holes. drilling tool, boring tool, rotary tool, auger, gimlet, awl, bradawl, hydraulic drill a tool or machine with a rotating cutting tip or reciprocating hammer or chisel, used for making holes. drill drilling tool, boring tool, rotary tool, auger, gimlet, awl, bradawl, hydraulic drill Electrophoresis protocol is a subclass of laboratory protocol. Electrophoresis protocol is a step by step description of an electrophoresis procedure in which are recovered fragments of biomolecules separated by charge. Electrophoresis protocol is a subclass of laboratory protocol. Electrophoresis protocol is a step by step description of an electrophoresis procedure in which are recovered fragments of biomolecules separated by charge. electrophoresis protocol Proteinase K is commonly used in molecular biology to digest protein and remove contamination from preparations of nucleic acid. An enzyme that catalyzes the hydrolysis of keratin, and of other proteins with subtilisin-like specificity. It hydrolyses peptide amides. Endopeptidase K is from the mold Tritirachium album Limber. Proteinase K Endopeptidase K Protease K Tritirachium Alkaline Proteinase Tritirachium album serine proteinase Tritirachium album proteinase K National Drug File-Reference Terminology An enzyme that catalyzes the hydrolysis of keratin, and of other proteins with subtilisin-like specificity. It hydrolyses peptide amides. Endopeptidase K is from the mold Tritirachium album Limber. Definition source: National Drug File-Reference Terminology Example of usage: Proteinase K is commonly used in molecular biology to digest protein and remove contamination from preparations of nucleic acid. endopeptidase K Proteinase K Endopeptidase K Protease K Tritirachium Alkaline Proteinase Tritirachium album serine proteinase Tritirachium album proteinase K Enzimatic amplification protocol is a subclass of laboratory protocol. Enzimatic amplification protocol, is a step by step description of a procedure about the use of enzymes to increase the number of molecules from a material entity. Enzimatic amplification protocol is a subclass of laboratory protocol. Enzimatic amplification protocol, is a step by step description of a procedure about the use of enzymes to increase the number of molecules from a material entity. enzimatic amplification protocol Enzymes are biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified. Biocatalysts Enzymes MESH enzyme reagent Equipment and supplies list is a data set of the names or identifiers of the equipments and supplies that are part of materials section of a protocol. Equipment and supplies list is a data set of the names or identifiers of the equipments and supplies that are part of materials section of a protocol. equipment and supplies list Nalgene Cryogenic Tube, sterile, 1.2 ml. S1000 Thermal Cycler with 96-Deep Well Reaction Module. Equipment or supply name is a textual entity. Equipment or supply name is the name of equipment or supply. Equipment or supply name is a textual entity. Equipment or supply name is the name of equipment or supply. Example of usage: Nalgene Cryogenic Tube, sterile, 1.2 ml. S1000 Thermal Cycler with 96-Deep Well Reaction Module. equipment or supplies name 70% ethanol A homogeneous mixture of ethanol and water. http://cameochemicals.noaa.gov/chemical/19240 A homogeneous mixture of ethanol and water. Definition source: http://cameochemicals.noaa.gov/chemical/19240 Example of usage: 70% ethanol ethanol solution An experimental protocol is a sequence of tasks and operations executed to perform experimental research. The protocols often include equipment, reagents, critical steps, troubleshooting, tips and all the information that facilitates reusability. An experimental protocol is a sequence of tasks and operations executed to perform experimental research. The protocols often include equipment, reagents, critical steps, troubleshooting, tips and all the information that facilitates reusability. experimental protocol The final measured concentration of a compound in a substance. Last concentration Adopted from NCI thesaurus The final measured concentration of a compound in a substance. Definition source: Adopted from NCI thesaurus final concentration Last concentration Keep away from sources of ignition. Reference: Nature Protocols Easily ignited. Inflammable http://wordnetweb.princeton.edu/perl/webwn?s=flammable Easily ignited. Definition source: http://wordnetweb.princeton.edu/perl/webwn?s=flammable Example of usage: Keep away from sources of ignition. flammable Inflammable Freezer milling is a type of cryogenic milling that uses a solenoid to mill samples. The solenoid moves the grinding media back and forth inside the vial, grinding the sample down to analytical fineness. Cryogenic grinding, freezer grinding, cryomilling, freezer mill Freezer milling is a type of cryogenic milling that uses a solenoid to mill samples. The solenoid moves the grinding media back and forth inside the vial, grinding the sample down to analytical fineness. freezer milling Cryogenic grinding, freezer grinding, cryomilling, freezer mill Shearing is caused by high pressure when sample is forced through a small hole. french press Shearing is caused by high pressure when sample is forced through a small hole. french pressure cell press french press GeneAmp PCR Buffer is optimized for use with the enzyme AmpliTaq DNA Polymerase. GeneAmp 10X PCR Buffer I GeneAmp 10X PCR Buffer II GeneAmp10X PCR Gold Buffer GeneAmp PCR Buffer I GeneAmp PCR Buffer II GeneAmp PCR Gold Buffer GeneAmp PCR Buffer is optimized for use with the enzyme AmpliTaq DNA Polymerase. GeneAmp PCR Buffer GeneAmp 10X PCR Buffer I GeneAmp 10X PCR Buffer II GeneAmp10X PCR Gold Buffer GeneAmp PCR Buffer I GeneAmp PCR Buffer II GeneAmp PCR Gold Buffer A gene-specific primer is a short strand of nucleic acid that hybridizes only to sequences exactly complementary to the primer sequence. gene-specific primers Gene-Specific Primer Gene-specific primers Gene-specific primer gene specific primers gene specific primer Gene specific primers Gene specific primer Gene Specific Primer GSP Sequence Specific Primers Sequence-Specific Primers SSPs PERSON: Olga Giraldo A gene-specific primer is a short strand of nucleic acid that hybridizes only to sequences exactly complementary to the primer sequence. gene-specific primer gene-specific primers Gene-Specific Primer Gene-specific primers Gene-specific primer gene specific primers gene specific primer Gene specific primers Gene specific primer Gene Specific Primer GSP Sequence Specific Primers Sequence-Specific Primers SSPs Geno grinder is a plant and animal tissue homogenizer used for high-throughput applications involving sample preparation for DNA, RNA, and protein extractions, pesticide residue analysis, and more. Geno/Grinder GenoGrinder GenoGrinder machine genogrinder genogrinder machine Geno grinder is a plant and animal tissue homogenizer used for high-throughput applications involving sample preparation for DNA, RNA, and protein extractions, pesticide residue analysis, and more. geno grinder Geno/Grinder GenoGrinder GenoGrinder machine genogrinder genogrinder machine A diol in which the two hydroxy groups are on different carbon atoms, usually but not necessarily adjacent. Glykol glykol glycols CHEBI glycol reagent Put the number of seed indicated by the kit protocol in the grinding machine and grind the seed to a powder. Grinding machine is a equipment. Grinding machine is a machine used to grind grains and leaves. Grinding device Grinding machine is a equipment. Grinding machine is a machine used to grind grains and leaves. Example of usage: Put the number of seed indicated by the kit protocol in the grinding machine and grind the seed to a powder. grinding machine Grinding device guanidinium thiocyanate-phenol is a mixture used in RNA/DNA/protein extraction. guanidine thiocyanate-phenol guanidine thiocyanate-phenol solution guanidinium thiocyanate-phenol solution TRIzol TRI reagent Trisure STAT-60 guanidinium thiocyanate-phenol is a mixture used in RNA/DNA/protein extraction. guanidinium thiocyanate-phenol guanidine thiocyanate-phenol guanidine thiocyanate-phenol solution guanidinium thiocyanate-phenol solution TRIzol TRI reagent Trisure STAT-60 HINT: Mix well by vortex before to use. HINT: ADD NaOH to WATER to avoid splashing. A hint is a message given to a user of a protocol that will help to perform the experiment. A hint is a message given to a user of a protocol that will help to perform the experiment. Example of usage: HINT: Mix well by vortex before to use. HINT: ADD NaOH to WATER to avoid splashing. hint homogenized tissue is a tissue that is brought to a state such that all fractions of the tissue are equal in composition. homogenized tissue is a tissue that is brought to a state such that all fractions of the tissue are equal in composition. homogenized tissue A homogenizer is a equipment of laboratory used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Many different models have been developed using various physical technologies for disruption. https://en.wikipedia.org/wiki/Homogenizer A homogenizer is a equipment of laboratory used for the homogenization of various types of material, such as tissue, plant, food, soil, and many others. Many different models have been developed using various physical technologies for disruption. Definition source: https://en.wikipedia.org/wiki/Homogenizer homogenizer Hot Start Taq DNA Polymerase is a mixture of Taq DNA Polymerase and an aptamer-based inhibitor. HotStarTaq DNA Polymerase HotStarTaq Hot Start DNA Polymerase Hot Start Taq Taq Hot Start DNA Polymerase Taq-star enzyme Taq-star DNA polymerase TaqStar Hot-Start Taq DNA polymerase https://www.neb.com/products/m0495-hot-start-taq-dna-polymerase Hot Start Taq DNA Polymerase is a mixture of Taq DNA Polymerase and an aptamer-based inhibitor. Definition source: https://www.neb.com/products/m0495-hot-start-taq-dna-polymerase Hot Start Taq DNA Polymerase HotStarTaq DNA Polymerase HotStarTaq Hot Start DNA Polymerase Hot Start Taq Taq Hot Start DNA Polymerase Taq-star enzyme Taq-star DNA polymerase TaqStar Hot-Start Taq DNA polymerase Housing condition protocol is a protocol that defines instructions about the environmental conditions and handling of experimental organims. Housing condition protocol is a protocol that defines instructions about the environmental conditions and handling of experimental organims. housing condition protocol Infection protocol is a protocol used in parasitology experiments and defines instructions on how carry out the infection of a organism that acts as host. Infection protocol is a protocol used in parasitology experiments and defines instructions on how carry out the infection of a organism that acts as host. infection protocol Introduction section is part of a document. In the context of a protocol, this section show to reader about essential components of the protocol. So, the scientific community could make a decision as to the suitability of the protocol to their experimental problem.This section must include: applications of the protocol, comparison with other protocols, development of the protocol, limitations and purpose. Introduction section is part of a document. In the context of a protocol, this section show to reader about essential components of the protocol. So, the scientific community could make a decision as to the suitability of the protocol to their experimental problem.This section must include: applications of the protocol, comparison with other protocols, development of the protocol, limitations and purpose. introduction section Universal Linker Kit, laboratory kit that allows customization of protein microarrays. A set of chemical substances, articles or equipment needed for a specific purpose. A set of chemical substances, articles or equipment needed for a specific purpose. Example of usage: Universal Linker Kit, laboratory kit that allows customization of protein microarrays. kit Spectrum Plant Total RNA Kit, sufficient for 50 purifications. Kit name is a textual entity. Kit name is the name of a kit. Kit name is a textual entity. Kit name is the name of a kit. Example of usage: Spectrum Plant Total RNA Kit, sufficient for 50 purifications. kit name KlenTaq DNA Polymerase is missing the N-terminal portion of the gene, encoding Thermus aquaticus (Taq) DNA polymerase, leaving a highly active and even more thermal stable DNA polymerase activity. The missing N-terminal portion is homologous to the 5’→3’ exonuclease region of E. coli. DNA polymerase I. Cesium Klentaq Klentaq LA Klentaq Omni Klentaq Omniklentaq Omni Klentaq LA Omniklentaq-LA http://www.klentaq.com/products/klentaq KlenTaq DNA Polymerase is missing the N-terminal portion of the gene, encoding Thermus aquaticus (Taq) DNA polymerase, leaving a highly active and even more thermal stable DNA polymerase activity. The missing N-terminal portion is homologous to the 5’→3’ exonuclease region of E. coli. DNA polymerase I. Definition source: http://www.klentaq.com/products/klentaq KlenTaq DNA Polymerase Cesium Klentaq Klentaq LA Klentaq Omni Klentaq Omniklentaq Omni Klentaq LA Omniklentaq-LA A major problem faced both in this and other safflower transformation studies is the hyperhydration of transgenic shoots which result in the loss of a large proportion of transgenic shoots. Belide Srinivas., 2011 Limitation of the protocol is a subclass of textual entity where the possible limitations of the protocol should be discussed. It should be made clear in which situations the Protocol would be unreliable or otherwise unsuccessful. http://www.nature.com/nprot/info/gta.html Limitation of the protocol is a subclass of textual entity where the possible limitations of the protocol should be discussed. It should be made clear in which situations the Protocol would be unreliable or otherwise unsuccessful. Definition source: http://www.nature.com/nprot/info/gta.html Example of usage: A major problem faced both in this and other safflower transformation studies is the hyperhydration of transgenic shoots which result in the loss of a large proportion of transgenic shoots. Belide Srinivas., 2011 limitation of the protocol freeze-dried ground tissue freeze dried ground tissue lyophilized ground tissue freeze-dried ground tissue freeze dried ground tissue freeze-dried leaf freeze dried leaf lyophilized leaf tissue lyophilized leaf freeze-dried leaf freeze dried leaf lyophilized leaf tissue freeze-dried root freeze dried root lyophilized root tissue lyophilized root freeze-dried root freeze dried root lyophilized root tissue freeze-dried seed freeze dried seed lyophilized seed tissue lyophilized seed freeze-dried seed freeze dried seed lyophilized seed tissue lyophilized leaf, lyophilized root, lyophilized seed lyophilized tissue is a tissue dried by freezing in a high vacuum lyophilized tissue is a tissue dried by freezing in a high vacuum Example of usage: lyophilized leaf, lyophilized root, lyophilized seed lyophilized tissue A lysis buffer is a buffer solution used for the purpose of lysing cells for use in molecular biology experiments that analyze the compounds of the cells (e.g. western blot). Most lysis buffers contain salts (e.g. Tris-HCl or EDTA) to regulate the acidity and osmolarity of the lysate, while detergents (such as Triton X-100 or SDS) are added to break up membrane structures. In studies like DNA fingerprinting the lysis buffer is used for DNA isolation. Dish soap can be used in a pinch to break down the cell and nuclear membranes, allowing the DNA to be released. extraction buffer isolation buffer lysis solution lysate solution digestion buffer homogenization buffer extraction solution solubilizing buffer Digestion buffer Extraction buffer Extraction solution Homogenization buffer Isolation buffer Lysate solution Lysis buffer Lysis solution tissue lysis buffer https://en.wikipedia.org/wiki/Lysis_buffer A lysis buffer is a buffer solution used for the purpose of lysing cells for use in molecular biology experiments that analyze the compounds of the cells (e.g. western blot). Most lysis buffers contain salts (e.g. Tris-HCl or EDTA) to regulate the acidity and osmolarity of the lysate, while detergents (such as Triton X-100 or SDS) are added to break up membrane structures. In studies like DNA fingerprinting the lysis buffer is used for DNA isolation. Dish soap can be used in a pinch to break down the cell and nuclear membranes, allowing the DNA to be released. Definition source: https://en.wikipedia.org/wiki/Lysis_buffer lysis buffer extraction buffer isolation buffer lysis solution lysate solution digestion buffer homogenization buffer extraction solution solubilizing buffer Digestion buffer Extraction buffer Extraction solution Homogenization buffer Isolation buffer Lysate solution Lysis buffer Lysis solution tissue lysis buffer M-MLV reverse transcriptaseis an enzyme from the Moloney murine leukemia virus is a single 75 kDa monomer. Moloney Murine Leukemia Virus (M-MuLV) Reverse Transcriptase Moloney Murine Leukemia Virus (MMLV) Reverse Transcriptase Moloney Murine Leukemia Virus (M-MLV) Reverse Transcriptase Moloney Murine Leukemia Virus Reverse Transcriptase M-MuLV Reverse Transcriptase MMuLV Reverse Transcriptase MMLV Reverse Transcriptase MMLV RT M-MLV RT MMuLV M-MuLV RT http://link.springer.com/article/10.1007%2Fs10529-012-0904-9 M-MLV reverse transcriptaseis an enzyme from the Moloney murine leukemia virus is a single 75 kDa monomer. Definition source: http://link.springer.com/article/10.1007%2Fs10529-012-0904-9 M-MLV reverse transcriptase Moloney Murine Leukemia Virus (M-MuLV) Reverse Transcriptase Moloney Murine Leukemia Virus (MMLV) Reverse Transcriptase Moloney Murine Leukemia Virus (M-MLV) Reverse Transcriptase Moloney Murine Leukemia Virus Reverse Transcriptase M-MuLV Reverse Transcriptase MMuLV Reverse Transcriptase MMLV Reverse Transcriptase MMLV RT M-MLV RT MMuLV M-MuLV RT DNA purification MPDB buffer is a lysis buffer used during isolation of DNA. MPDB Buffer 2-methyl-2,4-pentanediol buffer MPDB MPDB-buffer MPDB buffer is a lysis buffer used during isolation of DNA. Example of usage: DNA purification MPDB buffer MPDB Buffer 2-methyl-2,4-pentanediol buffer MPDB MPDB-buffer Bio-Rad, Nalgene, Thermoscientific, Eppendorf, Falcon. Manufacturer is a subclass of material entity. Manufacturer is a person, enterprise, or entity that produces equipments, reagents, primers or other laboratory supplies. Example of usage: Bio-Rad, Nalgene, Thermoscientific, Eppendorf, Falcon. manufacturer Manufacturer name is a subclass of textual entity. Manufacturer name is the name of a person, enterprise, or entity that produces equipments, reagents, primers or other laboratory supplies. Manufacturer name is a subclass of textual entity. Manufacturer name is the name of a person, enterprise, or entity that produces equipments, reagents, primers or other laboratory supplies. manufacturer name Materials section is part of a document. In the context of a protocol, this section should list the sample, buffers, reagents, consumables, equipments, kits, software etc., necessary for carrying out your technique. Materials section is part of a document. In the context of a protocol, this section should list the sample, buffers, reagents, consumables, equipments, kits, software etc., necessary for carrying out your technique. materials section mechanical milling is a plant and animal tissue homogenizer used for applications involving sample preparation for DNA, RNA, and protein extractions. mechanical mill mechanical milling is a plant and animal tissue homogenizer used for applications involving sample preparation for DNA, RNA, and protein extractions. mechanical milling mechanical mill Protein purification The membrane extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. Membrane extraction buffer is a buffer used for membrane protein solubilization. MEB MEB buffer Membrane Extraction Buffer MEB extraction buffer https://www.embl.de/pepcore/pepcore_services/protein_purification/extraction_clarification/solubilisation_membrane_proteins/ The membrane extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. Membrane extraction buffer is a buffer used for membrane protein solubilization. Definition source: https://www.embl.de/pepcore/pepcore_services/protein_purification/extraction_clarification/solubilisation_membrane_proteins/ Example of usage: Protein purification membrane extraction buffer MEB MEB buffer Membrane Extraction Buffer MEB extraction buffer Methods section is part of a document. This is the section where the protocol is presented. Methods section is part of a document. This is the section where the protocol is presented. methods section Pour off supernatant into 1.5 ml microfuge tube. Microcentrifuge tube is a supply. Microcentrifuge tubes are plastic tubes with capacities from 250 ul to 2.0 ml. Microcentrifuge tips microfuge tube http://en.wikipedia.org/wiki/Laboratory_centrifuge#Centrifuge_tubes Microcentrifuge tube is a supply. Microcentrifuge tubes are plastic tubes with capacities from 250 ul to 2.0 ml. Definition source: http://en.wikipedia.org/wiki/Laboratory_centrifuge#Centrifuge_tubes Example of usage: Pour off supernatant into 1.5 ml microfuge tube. microcentrifuge tube Microcentrifuge tips microfuge tube micropestle is a very small pestle used for tissue homogenization. Some micropestles have an end which fits 1.5mL microcentrifuge tube; others micropestles have an end which fits 2ml microcentrifuge tube. micropestle is a very small pestle used for tissue homogenization. Some micropestles have an end which fits 1.5mL microcentrifuge tube; others micropestles have an end which fits 2ml microcentrifuge tube. micropestle Mixer mill is a machine used for grinding dry, brittle samples. Mixer/Mill MixerMill shaker mill high-energy ball mill Mixer mill is a machine used for grinding dry, brittle samples. mixer mill Mixer/Mill MixerMill shaker mill high-energy ball mill A mortar and pestle is a device used to crushing and grinding tissue into a fine powder. mortar grinding machine mortar grinder pestle and mortar https://en.wikipedia.org/wiki/Mortar_and_pestle A mortar and pestle is a device used to crushing and grinding tissue into a fine powder. Definition source: https://en.wikipedia.org/wiki/Mortar_and_pestle mortar and pestle mortar grinding machine mortar grinder pestle and mortar N-phenacylthiazolium bromide (PTB) is used during DNA extraction. This chemical compound has demonstrated to cleave Maillard products, thus freeing up DNA for PCR amplification. N-phenacylthiazolium bromide is a compound that breaks cross-links in Advanced glycation end products. N-phenacyl thiazolium bromide N-Phenacylthiazolium Bromide N-Phenacylthiazolium bromide PTB https://en.wikipedia.org/wiki/Phenacyl N-phenacylthiazolium bromide is a compound that breaks cross-links in Advanced glycation end products. Definition source: https://en.wikipedia.org/wiki/Phenacyl Example of usage: N-phenacylthiazolium bromide (PTB) is used during DNA extraction. This chemical compound has demonstrated to cleave Maillard products, thus freeing up DNA for PCR amplification. N-phenacylthiazolium bromide N-phenacyl thiazolium bromide N-Phenacylthiazolium Bromide N-Phenacylthiazolium bromide PTB The nuclear extraction buffer plus MNase is part of the Subcellular Protein Fractionation Kit for Tissues. Nuclear extraction buffer with micrococcal nuclease releases chromatin-bound nuclear proteins. nuclear extraction buffer with micrococcal nuclease NEB + MNase nuclear extraction buffer plus micrococcal nuclease (chromatin-bound fraction) https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html The nuclear extraction buffer plus MNase is part of the Subcellular Protein Fractionation Kit for Tissues. Nuclear extraction buffer with micrococcal nuclease releases chromatin-bound nuclear proteins. Definition source: https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html nuclear extraction buffer plus MNase nuclear extraction buffer with micrococcal nuclease NEB + MNase nuclear extraction buffer plus micrococcal nuclease (chromatin-bound fraction) NH4 Buffer is an ready-to-use buffer for PCR using Taq DNA Polymerases (both recombinant and native). Taq Buffer with (NH4)2SO4 NH4 Buffer PERSON:Olga Giraldo NH4 Buffer is an ready-to-use buffer for PCR using Taq DNA Polymerases (both recombinant and native). NH4 buffer Taq Buffer with (NH4)2SO4 NH4 Buffer avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition. When handling , wear gloves. Reference: Nature Protocols Poisonous to nerves or nerve cells. http://wordnetweb.princeton.edu/perl/webwn?s=neurotoxic Poisonous to nerves or nerve cells. Definition source: http://wordnetweb.princeton.edu/perl/webwn?s=neurotoxic Example of usage: avoid contact with skin, eyes or mucous membranes; keep away from sources of ignition. When handling , wear gloves. neurotoxic The nuclear extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. The nuclear extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. nuclear extraction buffer Nucleic acid extraction protocol is a subclass of laboratory protocol. A nucleic acid extraction protocol is a step by step description of a procedure used to recover the nucleic acid fraction of an input material entity. Nucleic acid extraction protocol is a subclass of laboratory protocol. A nucleic acid extraction protocol is a step by step description of a procedure used to recover the nucleic acid fraction of an input material entity. nucleic acid extraction protocol oligo (dT) primer is a short sequence of deoxy-thymine nucleotides. Oligo (dT) is tagged as a complementary primer which binds to the poly-A tail providing a free 3'-OH end that can be extended by reverse transcriptase to create the complementary DNA strand. Oligo dT primer Oligo dT primers oligo dT primer oligo(dT) primer oligo(dT) primers Oligo(dT) primer oligo (dT) primers https://en.wikipedia.org/wiki/CDNA_library oligo (dT) primer is a short sequence of deoxy-thymine nucleotides. Oligo (dT) is tagged as a complementary primer which binds to the poly-A tail providing a free 3'-OH end that can be extended by reverse transcriptase to create the complementary DNA strand. Definition source: https://en.wikipedia.org/wiki/CDNA_library oligo (dT) primer Oligo dT primer Oligo dT primers oligo dT primer oligo(dT) primer oligo(dT) primers Oligo(dT) primer oligo (dT) primers protocol outcome is a textual entity that is an outcome or expected result by a protocol execution. protocol outcome is a textual entity that is an outcome or expected result by a protocol execution. outcome of the protocol PCR amplification is used in molecular biology to amplify a single copy or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. It is a way to amplify a focused segment of DNA, useful for such purposes as the diagnosis and monitoring of genetic diseases, identification of criminals (in the field of forensics), and studying the function of a targeted segment of DNA. Definition source: http://learn.genetics.utah.edu/content/labs/pcr/ PCR amplification Taqman buffer, PCR Buffer with (or without) MgCl2 PCR buffer is a solution that provide a suitable chemical environment for optimum activity and stability of the DNA polymerase PCR Buffer PCR enzyme buffer https://en.wikipedia.org/wiki/Polymerase_chain_reaction PCR buffer is a solution that provide a suitable chemical environment for optimum activity and stability of the DNA polymerase. Definition source: https://en.wikipedia.org/wiki/Polymerase_chain_reaction Example of usage: Taqman buffer, PCR Buffer with (or without) MgCl2 PCR buffer PCR Buffer PCR enzyme buffer PAUSE POINT: Can be left overnight at 48 C or frozen for up to a month at -20 C. Pause point is the point were the protocol naturally breaks into separate stages. Pause point is the point were the protocol naturally breaks into separate stages. Example of usage: PAUSE POINT: Can be left overnight at 48 C or frozen for up to a month at -20 C. pause point The pellet extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. Pellet extraction buffer is used to isolate cytoskeletal proteins. PEB PEB buffer The pellet extraction buffer is part of the Subcellular Protein Fractionation Kit for Tissues. Pellet extraction buffer is used to isolate cytoskeletal proteins. pellet extraction buffer PEB PEB buffer Phenacyl bromide reagent is a reagent that has formula C8H7BrO. 2-bromo-1-phenylethanone omega-Bromoacetophenone alpha-Bromoacetophenone Bromomethyl phenyl ketone 2-Bromoacetophenone CHEBI phenacyl bromide reagent A mixture consisting of equal parts of equilibrated phenol and chloroform:isoamyl alcohol (24:1) is frequently used to remove proteins from preparations of nucleic acids. The chloroform denatures proteins and facilitates the separation of the aqueous and organic phases, and the isoamyl alcohol reduces foaming during extraction. http://cshprotocols.cshlp.org/content/2006/1/pdb.rec8282.full?text_only=true A mixture consisting of equal parts of equilibrated phenol and chloroform:isoamyl alcohol (24:1) is frequently used to remove proteins from preparations of nucleic acids. The chloroform denatures proteins and facilitates the separation of the aqueous and organic phases, and the isoamyl alcohol reduces foaming during extraction. Definition source: http://cshprotocols.cshlp.org/content/2006/1/pdb.rec8282.full?text_only=true Phenol:Chloroform:Isoamyl alcohol PBS has many uses because it is isotonic and non-toxic to cells. It can be used to dilute substances. It is used to rinse containers containing cells. PBS can be used as a diluent in methods to dry biomolecules, as water molecules within it will be structured around the substance (protein, for example) to be ‘dried’ and immobilized to a solid surface. The thin film of water that binds to the substance prevents denaturation or other conformational changes. Carbonate buffers may be used for the same purpose but with less effectiveness. PBS can be used to take a reference spectrum when measuring the protein adsorption in ellipsometry (http://protocolsonline.com/recipes/phosphate-buffered-saline-pbs/) Phosphate buffered saline (PBS) is a non toxic solution used in many biological laboratories. Unlike water, PBS prevents cells rupturing or shrivelling up due to osmosis. PBS can be used for the extraction of spermatozoa and cells from swabs and PBS does not affect subsequent DNA profiling. PBS Phosphate Buffered Saline phosphate-buffered saline http://www.maths.lancs.ac.uk/~lucy/publications/Martin-Pirie-Ford-Callaghan-McTurk-Lucy-Scrimger-2006.pdf Phosphate buffered saline (PBS) is a non toxic solution used in many biological laboratories. Unlike water, PBS prevents cells rupturing or shrivelling up due to osmosis. PBS can be used for the extraction of spermatozoa and cells from swabs and PBS does not affect subsequent DNA profiling. Definition source: http://www.maths.lancs.ac.uk/~lucy/publications/Martin-Pirie-Ford-Callaghan-McTurk-Lucy-Scrimger-2006.pdf phosphate buffered saline Example of usage: PBS has many uses because it is isotonic and non-toxic to cells. It can be used to dilute substances. It is used to rinse containers containing cells. PBS can be used as a diluent in methods to dry biomolecules, as water molecules within it will be structured around the substance (protein, for example) to be ‘dried’ and immobilized to a solid surface. The thin film of water that binds to the substance prevents denaturation or other conformational changes. Carbonate buffers may be used for the same purpose but with less effectiveness. PBS can be used to take a reference spectrum when measuring the protein adsorption in ellipsometry (http://protocolsonline.com/recipes/phosphate-buffered-saline-pbs/) PBS Phosphate Buffered Saline phosphate-buffered saline Equipment used for cell disruption methods. Some examples: mortar and pestle; handheld device (for example, Dounce and Potter-Elvehjem homogenizers), motorized devices (for example, blenders). physical disruption equipment and supplies Pluronic F-68 Pluronic F68 Pluronic F68 is used in cell culture as a stabilizer of cell membranes protecting from membrane shearing and additionally acts as an anti-foaming agent. Definition source: http://bit.do/thermofisher-PluronicF68 pluronic F-68 Pluronic F-68 Pluronic F68 PCR protocol is a step by step description of the procedure to amplify a particular DNA sequence. PCR protocol is a step by step description of the procedure to amplify a particular DNA sequence. polimerase chain reaction protocol precipitation of DNA poly ethylene glycol is a polymer composed of repeating ethyleneoxy units. polyethylene oxide PEO alpha,omega-hydroxypoly(ethylene oxide) Macrogol alpha-hydro-omega-hydroxypoly(oxy-1,2-ethanediyl) Polyethylene glycol 1,2-ethanediol homopolymer Polyaethylenglykole Glycols, polyethylene polyoxyethylene polyethylene glycols ethylene glycol homopolymer (C2H4O)n poly(ethyleneoxide) polyethylene glycol alpha-hydro-omega-hydroxypoly(oxyethylene) Polyaethylenglykol poly(oxyethylene) PEG POE Poly(ethylene glycol) CHEBI example of usage source: chrome-extension://padcapdkhelngdelppbbjmkmkfceoikg/content/pdf/viewer/viewer.html?file=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC333871%2Fpdf%2Fnar00242-0172.pdf poly ethylene glycol reagent Polytron homogenizer is a instrument used for pulverizing plant and animal tissue, grain and seed, soil extraction, DNA/RNA extraction. polytron poly-tron mixer polytron mixer Polytron homogenizer is a instrument used for pulverizing plant and animal tissue, grain and seed, soil extraction, DNA/RNA extraction. polytron homogenizer polytron poly-tron mixer polytron mixer PVP (polyvinylpyrrolidone) is added to remove phenolic compounds from plant DNA extracts. PVP precipitates polyphenolics. A vinyl polymer composed of repeating -CH2-CR- units where R is a 2-oxopyrrolidin-1-yl group. poly(vinylpyrrolidone) poly[1-(2-oxopyrrolidin-1-yl)ethylene] poly(vinylpyrrolidone) N-Vinylbutyrolactam polymer Vinylpyrrolidone polymer Poly(N-vinyl-2-pyrrolidone) N-Vinylpyrrolidinone polymer Poly(1-vinyl-2-pyrrolidinone) Polividone polyvidone Poly(N-vinyl-2-pyrrolidinone) 1-Vinyl-2-pyrrolidone polymer 1-Ethenyl-2-pyrrolidinone homopolymer Poly-N-vinyl pyrrolidone; Poly(1-ethenyl-2-pyrrolidinone) Poly(1-vinylpyrrolidinone); Poly(N-vinylbutyrolactam) Poly(1-vinyl-2-pyrrolidinone) homopolymer PVPON PVP PVP40 PVP-40 PVP 40 PVP10 PVP-10 PVP 10 poly(N-vinyl pyrrolidone) Crospovidonum Polyvinylpyrrolidone Povidone Polyvidonum Poly(N-vinylpyrrolidinone) 1-Vinyl-2-pyrrolidinone homopolymer Poly(1-vinyl-2-pyrrolidone) Polividona polyvinylpyrrolidone N-Vinyl-2-pyrrolidone polymer N-Vinylpyrrolidone polymer Vinylpyrrolidinone polymer poly(N-vinylpyrrolidone) 1-Ethenyl-2-pyrrolidinone polymers 1-Vinyl-2-pyrrolidinone polymer (C6H9NO)n Poly(1-(2-oxo-1-pyrrolidinyl)ethylene) CHEBI A vinyl polymer composed of repeating -CH2-CR- units where R is a 2-oxopyrrolidin-1-yl group. Definition source: CHEBI Example of usage: PVP (polyvinylpyrrolidone) is added to remove phenolic compounds from plant DNA extracts. PVP precipitates polyphenolics. polyvinylpyrrolidone poly(vinylpyrrolidone) poly[1-(2-oxopyrrolidin-1-yl)ethylene] poly(vinylpyrrolidone) N-Vinylbutyrolactam polymer Vinylpyrrolidone polymer Poly(N-vinyl-2-pyrrolidone) N-Vinylpyrrolidinone polymer Poly(1-vinyl-2-pyrrolidinone) Polividone polyvidone Poly(N-vinyl-2-pyrrolidinone) 1-Vinyl-2-pyrrolidone polymer 1-Ethenyl-2-pyrrolidinone homopolymer Poly-N-vinyl pyrrolidone; Poly(1-ethenyl-2-pyrrolidinone) Poly(1-vinylpyrrolidinone); Poly(N-vinylbutyrolactam) Poly(1-vinyl-2-pyrrolidinone) homopolymer PVPON PVP PVP40 PVP-40 PVP 40 PVP10 PVP-10 PVP 10 poly(N-vinyl pyrrolidone) Crospovidonum Polyvinylpyrrolidone Povidone Polyvidonum Poly(N-vinylpyrrolidinone) 1-Vinyl-2-pyrrolidinone homopolymer Poly(1-vinyl-2-pyrrolidone) Polividona polyvinylpyrrolidone N-Vinyl-2-pyrrolidone polymer N-Vinylpyrrolidone polymer Vinylpyrrolidinone polymer poly(N-vinylpyrrolidone) 1-Ethenyl-2-pyrrolidinone polymers 1-Vinyl-2-pyrrolidinone polymer (C6H9NO)n Poly(1-(2-oxo-1-pyrrolidinyl)ethylene) Place bags in a portable ice chest or other container with ice to keep samples cool. A portable ice chest is a supply. A cooler, cool box, portable ice chest, chilly bin (in New Zealand), or esky (Australia) most commonly is an insulated box used to keep the things cool. cooler cool box chilly bin esky http://en.wikipedia.org/wiki/Cooler A portable ice chest is a supply. A cooler, cool box, portable ice chest, chilly bin (in New Zealand), or esky (Australia) most commonly is an insulated box used to keep the things cool. Definition source: http://en.wikipedia.org/wiki/Cooler Example of usage: Place bags in a portable ice chest or other container with ice to keep samples cool. portable ice chest cooler cool box chilly bin esky Any alkali metal salt having potassium(1+) as the cation. potassium salts Kaliumsalze Kaliumsalz CHEBI potassium salt reagent Shearing is caused by a PTFE- coated pestle that is manually or mechanically driven into a conical vessel Shearing is caused by a PTFE- coated pestle that is manually or mechanically driven into a conical vessel potter-elvehjem homogenizer pulverized leaf pulverized leaf tissue powdered leaf tissue powdered leaf pulverized leaf pulverized leaf tissue powdered leaf tissue pulverized root pulverized root tissue powdered root tissue powdered root pulverized root pulverized root tissue powdered root tissue pulverized seed pulverized seed tissue powdered seed tissue powdered seed pulverized seed pulverized seed tissue powdered seed tissue Grind the seed to a powder. Transfer the powdered seed to a container and weigh the specified amount. Powdered tissue is a material entity. Powdered tissue is a tissue that has been pulverirized. pulverized tissue Powdered tissue is a material entity. Powdered tissue is a tissue that has been pulverirized. Example of usage: Grind the seed to a powder. Transfer the powdered seed to a container and weigh the specified amount. powdered tissue pulverized tissue precipitation reaction, is the third basic step in a DNA extraction. This is commonly achieved by ice-cold ethanol, or isopropanol, or phenol-chloroform, or by using minicolumn. precipitation reaction, is the third basic step in a DNA extraction. This is commonly achieved by ice-cold ethanol, or isopropanol, or phenol-chloroform, or by using minicolumn. precipitation reaction Oligos used in PCR. A primer is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis. Primer primers Primers http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29 A primer is a short strand of nucleic acid that serves as a starting point for DNA or RNA synthesis. Definition source: http://en.wikipedia.org/wiki/Primer_%28molecular_biology%29 Example of usage: Oligos used in PCR. primer Primer primers Primers CII-fw, CII-rv. Primer name is a textual entity. Primer name is the name of a primer. Primer name is a textual entity. Primer name is the name of a primer. Example of usage: CII-fw, CII-rv. primer name 5′-GAATGATGTACCACCTTTG-3′ Primer sequence is a textual entity. Primer sequence is a serie ordered of bases coded as letters (A,C,G,T) without spaces, that identify to a particular primer. Primer sequence is a textual entity. Primer sequence is a serie ordered of bases coded as letters (A,C,G,T) without spaces, that identify to a particular primer. Example of usage: 5′-GAATGATGTACCACCTTTG-3′ primer sequence Is a DNA that suffers changes during a laboratory procedure. Is a DNA that suffers changes during a laboratory procedure. processed DNA Is a RNA that suffers changes during a laboratory procedure. Is a RNA that suffers changes during a laboratory procedure. processed RNA Protein extraction protocol is a subclass of laboratory protocol. Protein extraction is an extraction where the desired output material is protein. Protein isolation protocol Protein extraction protocol is a subclass of laboratory protocol. Protein extraction is an extraction where the desired output material is protein. protein extraction protocol Protein isolation protocol protein precipitation buffer Any number that identifies a specific experimental protocol protocol identifier A protocol instruction should have sufficient level of detail and quantitative information to communicate it between domain experts, so that different domain experts will reliably be able to independently reproduce the procedure. EFO protocol instruction The extraction procedure precisely followed that of Lisec et al. (2006), which was developed from the protocol of Fiehn et al. (2000a). Allwood J. W., 2009 Provenance of the protocol is a subclass of textual entity. Provenance of the protocol include references to key papers where the protocol has been used previously. Indicate if your protocol is the result of modify a previous one or if it is the result of reuse steps of several (more than 1) protocols. Provenance of the protocol is a subclass of textual entity. Provenance of the protocol include references to key papers where the protocol has been used previously. Indicate if your protocol is the result of modify a previous one or if it is the result of reuse steps of several (more than 1) protocols. Example of usage: The extraction procedure precisely followed that of Lisec et al. (2006), which was developed from the protocol of Fiehn et al. (2000a). Allwood J. W., 2009 provenance of the protocol publication is a magazine, or other publication, in which a resource was/will be published. publication is a magazine, or other publication, in which a resource was/will be published. publication Development of a method to isolate small RNAs from different plant species (...) that no need of first total RNA extraction and is not based on the commercially available TRIzol; Reagent or columns. Rosas-Cardenas, F.d.F., et al., A simple and efficient method for isolating small RNAs from different plant species. Plant Methods, 2011. 7(4): p. 7. The purpose of a protocol is a subclass of textual entity. Its role, is to enable readers to make a decision as to the suitability of the protocol to their experimental problem. The purpose of a protocol is a subclass of textual entity. Its role, is to enable readers to make a decision as to the suitability of the protocol to their experimental problem. Example of usage: Development of a method to isolate small RNAs from different plant species (...) that no need of first total RNA extraction and is not based on the commercially available TRIzol; Reagent or columns. Rosas-Cardenas, F.d.F., et al., A simple and efficient method for isolating small RNAs from different plant species. Plant Methods, 2011. 7(4): p. 7. purpose of the protocol Iron sulfide and many reactive metals including uranium, when powdered or thinly sliced. Pyrophoric materials are often water-reactive as well and will ignite when they contact water or humid air. They can be handled safely in atmospheres of argon or (with a few exceptions) nitrogen. Most pyrophoric fires should be extinguished with a Class D fire extinguisher for burning metals. A chemical substance that will ignite spontaneously in air at or below a temperature of 130 F (54.4 C). http://www.utexas.edu/safety/ehs/msds/glossary/?page=p A chemical substance that will ignite spontaneously in air at or below a temperature of 130 F (54.4 C). Definition source: http://www.utexas.edu/safety/ehs/msds/glossary/?page=p Example of usage: Iron sulfide and many reactive metals including uranium, when powdered or thinly sliced. Pyrophoric materials are often water-reactive as well and will ignite when they contact water or humid air. They can be handled safely in atmospheres of argon or (with a few exceptions) nitrogen. Most pyrophoric fires should be extinguished with a Class D fire extinguisher for burning metals. pyrophoric Derivatives of ammonium compounds, (NH4(+))Y(-), in which all four of the hydrogens bonded to nitrogen have been replaced with univalent (usually hydrocarbyl) groups. quaternary ammonium compounds quaternary ammonium salt quaternary ammonium salts quaternary ammonium compound CHEBI quaternary ammonium salt reagent RNA extraction protocol is a subclass of nucleic acid extraction protocol. RNA extraction protocol, is a step by step description of a procedure in which is recovered a fraction of RNA from a material entity. RNA isolation protocol RNA extraction protocol is a subclass of nucleic acid extraction protocol. RNA extraction protocol, is a step by step description of a procedure in which is recovered a fraction of RNA from a material entity. RNA extraction protocol RNA isolation protocol RNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix. RNA separated by molecular size is obtained after the aplication of electrical potential to move material through a defined matrix. RNA separated by molecular size Random primers are used for synthesizing large pools of cDNA. They are also ideal for non-polyadenylated RNA, such as bacterial RNA, because they anneal throughout the target molecule. Degraded transcripts such as FFPE samples and secondary structure within the RNA do not pose as big a problem with random primers as they do with gene-specific primers and oligo(dT) primers. https://www.thermofisher.com/es/en/home/life-science/pcr/reverse-transcription/rna-priming-strategies.html Random primers are used for synthesizing large pools of cDNA. They are also ideal for non-polyadenylated RNA, such as bacterial RNA, because they anneal throughout the target molecule. Degraded transcripts such as FFPE samples and secondary structure within the RNA do not pose as big a problem with random primers as they do with gene-specific primers and oligo(dT) primers. Definition source: https://www.thermofisher.com/es/en/home/life-science/pcr/reverse-transcription/rna-priming-strategies.html random primer Reagent list is a data set of the names or identifiers of the reagents (purchased ready-to-use), that are part of materials section of a protocol. Reagent list is a data set of the names or identifiers of the reagents (purchased ready-to-use), that are part of materials section of a protocol. reagent list Taq DNA Polymerase from Thermus aquaticus with 10X reaction buffer without MgCl2. Reagent name is a textual entity. Reagent name is the name of a reagent. Reagent name is a textual entity. Reagent name is the name of a reagent. Example of usage: Taq DNA Polymerase from Thermus aquaticus with 10X reaction buffer without MgCl2. reagent name recipe list is a data set of the names or identifiers of the recipes, that are part of materials section of a protocol. recipe list is a data set of the names or identifiers of the recipes, that are part of materials section of a protocol. recipe list Recipe name is a textual entity. Recipe name is the name of a solution, buffer, media, etc that is prepared in the laboratory. Recipe name is a textual entity. Recipe name is the name of a solution, buffer, media, etc that is prepared in the laboratory. recipe name Reference lists contain a complete list of all the sources (books, journal articles, websites, etc.) that you have cited directly in a document. That means that if there are in-text citations for a source there is a reference list entry, and vice versa. list of works cited Reference lists contain a complete list of all the sources (books, journal articles, websites, etc.) that you have cited directly in a document. That means that if there are in-text citations for a source there is a reference list entry, and vice versa. reference list list of works cited a central location in which experimental protocols are stored and managed. a central location in which experimental protocols are stored and managed. repository Title of the repository in which a resource was/will be stored and managed. Title of the repository in which a resource was/will be stored and managed. repository name Results section is part of a document. In the context of a protocol, this section should show the output of a protocol. Results section is part of a document. In the context of a protocol, this section should show the output of a protocol. results section HIV-1 reverse transcriptase M-MLV reverse transcriptase AMV reverse transcriptase A Reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. RNA-directed DNA-polymerase RNA-directed DNA polymerase RNA-dependent DNA-polymerase RNA-dependent DNA polymerase https://en.wikipedia.org/wiki/Reverse_transcriptase A Reverse transcriptase (RT) is an enzyme used to generate complementary DNA (cDNA) from an RNA template, a process termed reverse transcription. Definition source: https://en.wikipedia.org/wiki/Reverse_transcriptase Example of usage: HIV-1 reverse transcriptase M-MLV reverse transcriptase AMV reverse transcriptase reverse transcriptase RNA-directed DNA-polymerase RNA-directed DNA polymerase RNA-dependent DNA-polymerase RNA-dependent DNA polymerase In this step, total RNA or messenger RNA (mRNA) is first transcribed into complementary DNA (cDNA) by reverse transcriptase. In this step, total RNA or messenger RNA (mRNA) is first transcribed into complementary DNA (cDNA) by reverse transcriptase. reverse transcription reverse transcription PCR protocol is a step by step description of the procedure to reverse-transcribe and amplify RNA to cDNA. reverse transcription PCR protocol is a step by step description of the procedure to reverse-transcribe and amplify RNA to cDNA. reverse transcription PCR protocol a person who formally assesses or examines a document, for example, a protocol. reviewer role sample mills cover a broad range of sample preparation equipment and supplies. The range includes homogenizers, blenders and mills for the preparation of high-fat, high-moisture, dry, frozen and fibrous samples. sample mills cover a broad range of sample preparation equipment and supplies. The range includes homogenizers, blenders and mills for the preparation of high-fat, high-moisture, dry, frozen and fibrous samples. sample mill surfactant that enhances penetration of proteins and other macromolecules through cell membranes; it also has been used as an adjuvant for vaccines. Saponin is a compound containing one or more hydrophilic glycoside moieties combined with a lipophilic triterpenoid or steroid derivative. Found in particular abundance in plant species. sapogenin glycosides sapogenin glycoside saponins CHEBI Example of usage: surfactant that enhances penetration of proteins and other macromolecules through cell membranes; it also has been used as an adjuvant for vaccines. example usage source: http://www.sigmaaldrich.com/catalog/product/sigma/s4521?lang=en&region=CO Saponin is a compound containing one or more hydrophilic glycoside moieties combined with a lipophilic triterpenoid or steroid derivative. Found in particular abundance in plant species. Definition source: CHEBI saponin reagent sapogenin glycosides sapogenin glycoside saponins A N-alkylglycine that is the N-methyl derivative of glycine. It is an intermediate in the metabolic pathway of glycine. SARCOSINE Sarcosine MeGly (methylamino)acetic acid sarcosinic acid Sar N-Methylglycine (methylamino)ethanoic acid methylaminoacetic acid N-methylaminoacetic acid C3H7NO2 CHEBI A N-alkylglycine that is the N-methyl derivative of glycine. It is an intermediate in the metabolic pathway of glycine. Definition source: CHEBI sarcosine reagent SARCOSINE Sarcosine MeGly (methylamino)acetic acid sarcosinic acid Sar N-Methylglycine (methylamino)ethanoic acid methylaminoacetic acid N-methylaminoacetic acid C3H7NO2 An aqueous dilution of ethanol containing 75% ethanol by volume. 75% Ethyl Alcohol Ethyl Alcohol, 75% Alcohol, Ethyl 75% 75% (v/v) ethanol 75 per cent alcohol 75% RNase-free ethanol 75% RNase free ethanol 75% EtOH An aqueous dilution of ethanol containing 75% ethanol by volume. 75% ethanol 75% Ethyl Alcohol Ethyl Alcohol, 75% Alcohol, Ethyl 75% 75% (v/v) ethanol 75 per cent alcohol 75% RNase-free ethanol 75% RNase free ethanol 75% EtOH Sarkosyl is effective in solubilizing functionally active membrane proteins, the major use of Sarkosyl has been to isolate DNA and RNA. The principal reason for this is that Sarkosyl is highly efficient in dissociating nucleosomes and ribosomes. Sodium lauroyl sarcosinate also known as sarkosyl, is an ionic surfactant derived from sarcosine. In molecular biology experiments, sarkosyl is used to inhibit the initiation of DNA transcription. sarkosyl Sarkosyl sarcosyl Sarcosyl N-Lauroylsarcosine N-lauryl-sarcosine N-Dodecanoyl-N-methylglycine https://en.wikipedia.org/wiki/Sodium_lauroyl_sarcosinate Sodium lauroyl sarcosinate also known as sarkosyl, is an ionic surfactant derived from sarcosine. In molecular biology experiments, sarkosyl is used to inhibit the initiation of DNA transcription. Definition source: https://en.wikipedia.org/wiki/Sodium_lauroyl_sarcosinate Example of usage: Sarkosyl is effective in solubilizing functionally active membrane proteins, the major use of Sarkosyl has been to isolate DNA and RNA. The principal reason for this is that Sarkosyl is highly efficient in dissociating nucleosomes and ribosomes. Sodium lauroyl sarcosinate sarkosyl Sarkosyl sarcosyl Sarcosyl N-Lauroylsarcosine N-lauryl-sarcosine N-Dodecanoyl-N-methylglycine Any alkali metal salt having sodium(1+) as the cation. sodium salts Natriumsalze Natriumsalz CHEBI sodium salt reagent Software list is a data set of the names of softwares that are part of materials section of a protocol. Software list is a data set of the names of softwares that are part of materials section of a protocol. software list LightCycler 480 Software. Software name is a textual entity. Software name is the name of a software. Software name is a textual entity. Software name is the name of a software. Example of usage: LightCycler 480 Software. software name 3M NaOH (1L) Solution name is a textual entity. Solution name is the name of a liquid preparation that contains at least 2 chemical substances, one playing the role of solvent and the other one playing the role of solute. If is applicable, the name of the solution should including the follow information: solution concentration, and final volume. Solution name is a textual entity. Solution name is the name of a liquid preparation that contains at least 2 chemical substances, one playing the role of solvent and the other one playing the role of solute. If is applicable, the name of the solution should including the follow information: solution concentration, and final volume. Example of usage: 3M NaOH (1L) solution name specimen list is a data set of the names or identifiers of the specimens that are part of materials section of a protocol. sample list specimen list is a data set of the names or identifiers of the specimens that are part of materials section of a protocol. specimen list sample list Specimen name is a textual entity. Specimen name is the name of the organism, strain, line, ecotype, cultivar, etc. used in a protocol. sample name Specimen name is a textual entity. Specimen name is the name of the organism, strain, line, ecotype, cultivar, etc. used in a protocol. specimen name sample name A specimen preparation protocol is a protocol used in a biological experiment and defines instructions on how a specimen or sample should be treated in a given experimental scenario. sample preparation protocol A specimen preparation protocol is a protocol used in a biological experiment and defines instructions on how a specimen or sample should be treated in a given experimental scenario. specimen preparation protocol sample preparation protocol DNA purification Stain extraction buffer is a buffer used to digest and extract DNA. SEB SEB buffer Stain Extraction Buffer SEB extraction buffer Stain extraction buffer is a buffer used to digest and extract DNA. Example of usage: DNA purification stain extraction buffer SEB SEB buffer Stain Extraction Buffer SEB extraction buffer Stained DNA is a material entity. After the electrophoresis is complete, the molecules in the gel can be stained to make them visible. DNA may be visualized using ethidium bromide which, when intercalated into DNA, fluoresce under ultraviolet light. EtBr is a known mutagen, and safer alternatives are available, such as GelRed, which binds to the minor groove. SYBER Green I is another dsDNA stain. It is 25 times more sensitive, and possibly safer than EtBr, though there is no data addressing its mutagenicity or toxicity in humans. SYBER Safe is a variant of SYBR Green that has been shown to have low enough levels of mutagenicity and toxicity to be deemed nonhazardous waste under U.S. Federal regulations. If the molecules to be separated contain radioactivity, for example in DNA sequencing gel, an autoradiogram can be recorded of the gel. If the molecules to be separated not contain radioactivity in a DNA sequencing gel, it may be visualized using silver nitrate. http://en.wikipedia.org/wiki/Gel_electrophoresis Stained DNA is a material entity. After the electrophoresis is complete, the molecules in the gel can be stained to make them visible. DNA may be visualized using ethidium bromide which, when intercalated into DNA, fluoresce under ultraviolet light. EtBr is a known mutagen, and safer alternatives are available, such as GelRed, which binds to the minor groove. SYBER Green I is another dsDNA stain. It is 25 times more sensitive, and possibly safer than EtBr, though there is no data addressing its mutagenicity or toxicity in humans. SYBER Safe is a variant of SYBR Green that has been shown to have low enough levels of mutagenicity and toxicity to be deemed nonhazardous waste under U.S. Federal regulations. If the molecules to be separated contain radioactivity, for example in DNA sequencing gel, an autoradiogram can be recorded of the gel. If the molecules to be separated not contain radioactivity in a DNA sequencing gel, it may be visualized using silver nitrate. Definition source: http://en.wikipedia.org/wiki/Gel_electrophoresis stained DNA Any steroid substituted by at least one carboxy group.Annotations steroid acids CHEBI steroid acid reagent Any of naturally occurring compounds and synthetic analogues, based on the cyclopenta[a]phenanthrene carbon skeleton, partially or completely hydrogenated; there are usually methyl groups at C-10 and C-13, and often an alkyl group at C-17. By extension, one or more bond scissions, ring expansions and/or ring contractions of the skeleton may have occurred. Natural steroids are derived biogenetically from triterpenoids. CHEBI steroid reagent Store the buffer in foil covered dark coloured bottle at room temperature. Light sensitive. Can be used up to 2 months. Storage condition is a message given to a user of a protocol about the shelf life (maximum storage time) and temperature of storage of a buffer, reagent or solution. Storage condition is a message given to a user of a protocol about the shelf life (maximum storage time) and temperature of storage of a buffer, reagent or solution. Example of usage: Store the buffer in foil covered dark coloured bottle at room temperature. Light sensitive. Can be used up to 2 months. storage condition subcellular protein fractionation kit for tissues includes five cellular components to obtain proteins. https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html subcellular protein fractionation kit for tissues includes five cellular components to obtain proteins. Definition source: https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/protein-biology-application-notes/subcellular-protein-fractionation.html subcellular protein fractionation kit for tissues sulphate salts sulfate salts sulphates sulfates sulfate salt reagent sulphate salts sulfate salts sulphates sulfates SuperScript reverse transcriptase (RT) is a family of enzymes widely used for cDNA synthesis. Superscript II SuperScript II SuperScript III Superscript III SuperScript IV Superscript IV SuperScript II Reverse Transcriptase SuperScript III Reverse Transcriptase SuperScript IV Reverse Transcriptase Superscript II RT SuperScript II RT Superscript III RT SuperScript III RT SuperScript II Reverse Transcriptase (RT) SuperScript III Reverse Transcriptase (RT) SuperScript IV Reverse Transcriptase (RT) SuperScript reverse transcriptase (RT) is a family of enzymes widely used for cDNA synthesis. SuperScript reverse transcriptase Superscript II SuperScript II SuperScript III Superscript III SuperScript IV Superscript IV SuperScript II Reverse Transcriptase SuperScript III Reverse Transcriptase SuperScript IV Reverse Transcriptase Superscript II RT SuperScript II RT Superscript III RT SuperScript III RT SuperScript II Reverse Transcriptase (RT) SuperScript III Reverse Transcriptase (RT) SuperScript IV Reverse Transcriptase (RT) TaqMan buffer is PCR buffer with ROX added for florescence. TaqMan Buffer TaqMan master mix TaqMan Master Mix TaqMan Universal PCR Master Mix TaqMan universal PCR master mix http://cancer.ucsf.edu/_docs/cores/genome/protocols/TaqManBuffer.pdf TaqMan buffer is PCR buffer with ROX added for florescence. Definition source: http://cancer.ucsf.edu/_docs/cores/genome/protocols/TaqManBuffer.pdf TaqMan buffer TaqMan Buffer TaqMan master mix TaqMan Master Mix TaqMan Universal PCR Master Mix TaqMan universal PCR master mix Taq polymerase is a heat stable DNA-direct DNA polymerase from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of Polymerase Chain Reaction. Taq Polymerase Thermus aquaticus Polymerase Taq DNA Polymerase Taq1 Polymerase Taq pol Taq Enzyme Taq enzyme Taq DNA polymerase Thermostable DNA polymerase thermostable DNA polymerase thermophilic bacterium Thermus aquaticus Taq polymerase is a heat stable DNA-direct DNA polymerase from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of Polymerase Chain Reaction. taq polymerase Taq Polymerase Thermus aquaticus Polymerase Taq DNA Polymerase Taq1 Polymerase Taq pol Taq Enzyme Taq enzyme Taq DNA polymerase Thermostable DNA polymerase thermostable DNA polymerase thermophilic bacterium Thermus aquaticus Taq polymerase buffer is a solution formulated to provide efficient activation of the enzyme Taq DNA polymerase, resulting in PCR amplification. Taq DNA polymerase buffer Taq buffer Taq Buffer PERSON:Olga Giraldo Taq polymerase buffer is a solution formulated to provide efficient activation of the enzyme Taq DNA polymerase, resulting in PCR amplification. Taq polymerase buffer Taq DNA polymerase buffer Taq buffer Taq Buffer An aqueous dilution of ethanol containing 10% ethanol by volume. 10% Ethyl Alcohol Ethyl Alcohol, 10% Alcohol, Ethyl 10% 10% (v/v) ethanol 10 per cent alcohol 10% RNase-free ethanol 10% RNase free ethanol 10% EtOH An aqueous dilution of ethanol containing 10% ethanol by volume. 10% ethanol 10% Ethyl Alcohol Ethyl Alcohol, 10% Alcohol, Ethyl 10% 10% (v/v) ethanol 10 per cent alcohol 10% RNase-free ethanol 10% RNase free ethanol 10% EtOH Steps 1-3, 30 min.; Steps 6-7, 2 h Timing is a message used to indicate the approximate time that a step, or set of steps, could take. Timing is a message used to indicate the approximate time that a step, or set of steps, could take. Example of usage: Steps 1-3, 30 min.; Steps 6-7, 2 h timing Titanium Taq is a mixture consisting of a 5’ exonuclease-deficient Taq polymerase, and TaqStart Antibody, a monoclonal antibody which inhibits Taq at ambient temperatures. TaqStart Antibody provides automatic hot start PCR. TITANIUM Taq DNA Polymerase http://www.clontech.com/RO/Products/cDNA_Synthesis_and_Library_Construction/cDNA_and_Genomic_DNA/RACE-Ready_cDNA/ibcGetAttachment.jsp?cItemId=31113&fileId=5994516&sitex=10020:22372:US Titanium Taq is a mixture consisting of a 5’ exonuclease-deficient Taq polymerase, and TaqStart Antibody, a monoclonal antibody which inhibits Taq at ambient temperatures. TaqStart Antibody provides automatic hot start PCR. Definition source: http://www.clontech.com/RO/Products/cDNA_Synthesis_and_Library_Construction/cDNA_and_Genomic_DNA/RACE-Ready_cDNA/ibcGetAttachment.jsp?cItemId=31113&fileId=5994516&sitex=10020:22372:US Titanium Taq DNA Polymerase TITANIUM Taq DNA Polymerase Title of protocol is a subclass of textual entity. Title of protocol is the name of a protocol. Title of protocol is a subclass of textual entity. Title of protocol is the name of a protocol. title of the protocol Avoid inhalation, ingestion or contact with skin, eyes or mucous membranes. Reference: Nature Protocols Of or relating to or caused by a toxin or poison 'suffering from exposure to toxic substances' http://wordnetweb.princeton.edu/perl/webwn?s=toxic Of or relating to or caused by a toxin or poison 'suffering from exposure to toxic substances' Definition source: http://wordnetweb.princeton.edu/perl/webwn?s=toxic Example of usage: Avoid inhalation, ingestion or contact with skin, eyes or mucous membranes. toxic Problem: Low detection level for tested a miRNA (CT value>35) (Step 9 - 10) Possible reason: low abundant amiRNA, or low efficiency of low of polyA tailing and reverse transcription, or amplification condition is too stringent, or amiRNA is not correctly expressed or processed. Possible solutions: increase amount of cDNA template in PCR; use new polyA tailing and reverse transcription reagent, (...) or using low stringent PCR program; check PCR product sequence. A troubleshooting is a message given to a user of a protocol where common problems, possible causes, and solutions/methods of correction should be listed. A troubleshooting is a message given to a user of a protocol where common problems, possible causes, and solutions/methods of correction should be listed. Example of usage: Problem: Low detection level for tested a miRNA (CT value>35) (Step 9 - 10) Possible reason: low abundant amiRNA, or low efficiency of low of polyA tailing and reverse transcription, or amplification condition is too stringent, or amiRNA is not correctly expressed or processed. Possible solutions: increase amount of cDNA template in PCR; use new polyA tailing and reverse transcription reagent, (...) or using low stringent PCR program; check PCR product sequence. troubleshooting validator is a person who formally assesses or examines that the protocol can be understood and carried out correctly by users. validator role A macromolecule composed of repeating -CHR-CH2- units. vinyl polymer vinyl polymers CHEBI vinyl polymer macromolecule reagent handle in well-ventilated charcoal-filtered hood. Reference: Nature Protocols The property of a substance of changing readily from a solid or liquid to a vapor. The property of a substance of changing readily from a solid or liquid to a vapor. Example of usage: handle in well-ventilated charcoal-filtered hood. volatile Instrument used in mechanical lysis. Rotating blades grind and disperse cells and tissues https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/traditional-methods-cell-lysis.html Instrument used in mechanical lysis. Rotating blades grind and disperse cells and tissues. Definition source: https://www.thermofisher.com/es/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/traditional-methods-cell-lysis.html waring blender polytron wash solution This step is to wash any residual salt away from the pelleted DNA/RNA. http://bitesizebio.com/253/the-basics-how-ethanol-precipitation-of-dna-and-rna-works/ This step is to wash any residual salt away from the pelleted DNA/RNA. Definition source: http://bitesizebio.com/253/the-basics-how-ethanol-precipitation-of-dna-and-rna-works/ washing nucleic acids A general term denoting true fungi of the family Saccharomycetaceae that are widely distributed in substrates that contain sugars (such as fruits), and in soil, animal excreta, the vegetative parts of plants, etc. yeast cell The following could function as buffers when together in solution: i) Acetic acid (weak organic acid w/ formula CH3COOH) and a salt containing its conjugate base, the acetate anion (CH3COO-), such as sodium acetate (CH3COONa). ii) Pyridine (weak base w/ formula C5H5N) and a salt containing its conjugate acid, the pyridinium cation (C5H5NH+), such as Pyridinium Chloride. iii) Ammonia (weak base w/ formula NH3) and a salt containing its conjugate acid, the ammonium cation, such as Ammonium Hydroxide (NH4OH). A buffer is a solution that can resist pH change upon the addition of an acidic or basic components. It is able to neutralize small amounts of added acid or base, thus maintaining the pH of the solution relatively stable. This is important for processes and/or reactions which require specific and stable pH ranges. Buffer http://chemwiki.ucdavis.edu/Physical_Chemistry/Acids_and_Bases/Buffers A buffer is a solution that can resist pH change upon the addition of an acidic or basic components. It is able to neutralize small amounts of added acid or base, thus maintaining the pH of the solution relatively stable. This is important for processes and/or reactions which require specific and stable pH ranges. Definition source: http://chemwiki.ucdavis.edu/Physical_Chemistry/Acids_and_Bases/Buffers Example of usage: The following could function as buffers when together in solution: i) Acetic acid (weak organic acid w/ formula CH3COOH) and a salt containing its conjugate base, the acetate anion (CH3COO-), such as sodium acetate (CH3COONa). ii) Pyridine (weak base w/ formula C5H5N) and a salt containing its conjugate acid, the pyridinium cation (C5H5NH+), such as Pyridinium Chloride. iii) Ammonia (weak base w/ formula NH3) and a salt containing its conjugate acid, the ammonium cation, such as Ammonium Hydroxide (NH4OH). Buffer A single stranded oligo used for polymerase chain reaction. forward DNA primer DNA forward primer forward primer oligonucleotide forward primer oligo forward primer polynucleotide forward primer Forward primer forward primer sequence Upper primer upper primer sense primer forward DNA primer DNA forward primer forward primer oligonucleotide forward primer oligo forward primer polynucleotide forward primer forward primer sequence SNP Ontology This term is mapped to MGED. Do not obsolete without consulting MGED ontology. forward primer A single stranded oligo used for polymerase chain reaction. reverse primer oligonucleotide reverse primer sequence reverse primer oligo DNA reverse primer Reverse primer reverse DNA primer lower primer Lower primer antisense primer reverse primer oligonucleotide reverse primer sequence reverse primer oligo DNA reverse primer reverse primer reverse DNA primer SNP Ontology This term is mapped to MGED. Do not obsolete without consulting MGED ontology. reverse primer An expression of a bibliographic record in a specific format, that references a particular textual or data publication (or a work in preparation for publication). Each bibliographic reference is a list of items containing entities that describe aspects of the referenced work - for example authors, title, journal, publication year - selected from the bibliographic record. Note that because different journal styles may require omission of elements of the bibliographic record in references included in a paper's reference list (e.g. the title, the identifier, the names of the eighth and subsequent authors), and because errors can be introduced when an author creates a bibliographic reference, the bibliographic reference to a published work may not be a complete or fully accurate expression of the information contained within the authoritative bibliographic record for that work. BiRO, the Bibliographic Reference Ontology bibliographic reference A quantity is an informational entity that gives the magnitude of a property. SIO quantity A measurement value is a quantitative description that reflects the magnitude of some attribute. SIO measurement value A recipe is a set of instructions that describe how to prepare or make something. SIO recipe EFO BALB/c is an albino, laboratory-bred strain of the house mouse from which a number of common substrains are derived. BALB/c mice are distributed globally, and are among the most widely used inbred strains used in animal experimentation. Definition source: https://en.wikipedia.org/wiki/BALB/c BALB/c A/J is a mouse strain as described in Jackson Laboratory http://jaxmice.jax.org/strain/000646.html A/J is a mouse strain as described in Jackson Laboratory. Definition source: http://jaxmice.jax.org/strain/000646.html A/J C57BL/6 is a mouse strain as described in Jackson Laboratory strain index C57/B6 C57BL6 B6 C57Black6 CB57 C57Black/6 C57Bl C57Black C57/BL6 C57Bl\6 C57 C57B/6 C57 Black/6 EFO C57BL/6 A RNA extract that is the output of an extraction process in which total RNA from either whole cells or from specific cellular compartment(s)/organelle(s) are isolated from a specimenA RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. total RNA extract RNA extract A RNA extract that is the output of an extraction process in which total RNA from either whole cells or from specific cellular compartment(s)/organelle(s) are isolated from a specimenA RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen. total RNA total RNA extract RNA extract An inbred strain of mouse created in 1921 by C. C. Little at the Bussey Institute for Research in Applied Biology. EFO C57BL entity entity Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building Synonyms: endurant continuant Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities. dependent continuant Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time. Examples: a certain PDF file that exists in different and in several hard drives generically dependent continuant Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything. Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building Synonyms: substantial entity independent continuant Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. Examples: collection of random bacteria, a chair, dorsal surface of the body material entity Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property). Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee quality Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc. Synonyms: property, trope, mode specifically dependent continuant An alert message is information, such as a warning or a caution that can be ignored by an automatic agent. The goal is to remind or alert the user. EXACT alert message A caution is a message given to a user of a protocol about potentially dangerous properties of materials used in the experiment. EXACT caution Anthony J. Freemont Crispin J. Miller Ethyl alcohol Forceps Homogenizer blades DOI: 10.2144/000113260 protocol Id1 Isopropyl alcohol John A. Radford Kim M. Linton protocol available here: http://www.biotechniques.com/protocols/Peer-Reviewed_Protocols/Extraction-of-total-RNA-from-freshfrozen-tissue-FT/biotechniques-181792.html RNA extraction 1 Scalpel Scalpel holder Sian Dibben Sigma-Aldrich Stuart D. Pepper Tissue storage container Yvonne Hey Methods comparison for high-resolution transcriptional analysis of archival material on Affymetrix Plus 2.0 and Exon 1.0 microarrays application 1 author1 author list 1 Chloroform equipment list 1 equipment-list1 equipmentList1 equipment or supplies 1 equipment or supplies 2 equipment or supplies 3 equipment or supplies 4 equipment or supplies 5 The extraction method (steps 2–21) is taken from the method supplied with TRIzol reagent (Invitrogen, Paisley, UK). provenance 1 reagent list 1 reagentList1 Extraction of total RNA from fresh/frozen tissue (FT) title1 tumor tissue tumor-tissue