]> JERM:00137 JERM:00106 yeast 2 hybrid Two-hybrid screening (also known as yeast two-hybrid system or Y2H) is a molecular biology technique used to discover protein-protein interactions and protein-DNA interactions by testing for physical interactions JERM:00115 JERM:00120 JERM:00139 JERM:00021 descriptions of individual experiments JERM:00024 The assay_type hierarchy allows scientists to categorise their experimental assays, informatics analyses and computational models within SysMO An assay type describes the type of experiment being performed JERM:00010 all shareable entities in the SysMO SEEK are kinds of Assets JERM:00130 Chromatin Immunoprecipitation on Chip JERM:00086 JERM:00026 SysMO studies microorganisms. Each experiment is performed on cell cultures, so it is essential to record the type of culture in use each time JERM:00131 JERM:00058 JERM:00011 SEEK data files JERM:00038 JERM:00016 the experimental context for any of the SysMO assets JERM:00043 An experimental assay is an assay carried out in a laboratory JERM:00017 ExperimentalFactors are descriptors of the properties of the experiment. How the culture was prepared, what organism they are from, and what type of experiment was run JERM:00119 fluorescence recovery after photobleaching JERM:00027 factors studied describe what types of measurements were taken (i.e. what factors were expected to change during the experiment) also known as ExperimentalConditions JERM:00018 JERM:00121 JERM:00108 High Performance Liquid Chromatography. Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid High Performance Liquid Chromatography JERM:00122 JERM:00022 A high level description of the experimental work undertaken JERM:00123 JERM:00124 JERM:00140 JERM:00125 JERM:00126 JERM:00028 the entity under investigation (e.g. glucose) JERM:00012 computational models developed in SysMO JERM:00044 a model analysis type is a model "assay" type to classify the information contained within the model. The categories correspond to the existing categories in JWS Onnline, a tool for model simmulation JERM:00039 JERM:00040 JERM:00138 JERM:00042 JERM:00141 JERM:00093 the polymerase chain reaction (PCR) is a technique to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence. JERM:00142 JERM:00019 JERM:00020 JERM:00014 publication abstracts from SysMO JERM:00087 JERM:00116 sodium dodecyl sulfate polyacrylamide gel electrophoresis JERM:00127 JERM:00059 JERM:00015 Standard operating procedures and protocols from SysMO JERM:00041 JERM:00023 a collection of experiments designed to answer a particular biological question JERM:00128 JERM:00025 describes the technologies and/or techniques used in performing experiments JERM:00109 Ultra Performance Liquid Chromatography Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid Ultra Performance Liquid Chromatography JERM:00110 Affinity chromatography is based on selective non-covalent interaction between an analyte and specific molecules. It is often used in biochemistry in the purification of proteins bound to tags. These fusion proteins are labeled with compounds such as His-tags, biotin or antigens, which bind to the stationary phase specifically. affinity_purification JERM:00135 JERM:00094 laboratory techniques which involve separation by binding the molecules of interest JERM:00046 a bioinformatics analysis is an "assay" performed in silico, employing bioinformatics techniques to analyse biological data JERM:00113 JERM:00068 JERM:00048 JERM:00066 JERM:00047 a cheminformatics analysis is an "assay" performed in silico, employing cheminformatics techniques to analyse biological data JERM:00095 Chromatography is the collective term for a set of laboratory techniques for the separation of mixtures. It involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture based on differential partitioning between the mobile and stationary phases. JERM:00060 JERM:00031 JERM:00132 JERM:00037 JERM:00096 Electrophoresis is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field JERM:00083 JERM:00097 JERM:00049 JERM:00033 JERM:00069 JERM:00056 the dynamic changes of molecules within a cell over time JERM:00111 Gas chromatography (GC) is a separation technique in which the mobile phase is a gas JERM:00114 JERM:00112 size_exclusion_chromatography Size exclusion chromatography (SEC), also known as gel permeation chromatography or gel filtration chromatography, separates particles on the basis of size. It is generally a low resolution chromatography and thus it is often reserved for the final, "polishing" step of a purification. It is also useful for determining the tertiary structure and quaternary structure of purified proteins. JERM:00050 JERM:00088 JERM:00051 JERM:00081 JERM:00057 the study of the genome of an organism JERM:00061 JERM:00070 JERM:00098 JERM:00073 not sure about this one JERM:00045 an informatics analysis is an "assay" performed in silico, employing informatics techniques to analyse data JERM:00117 JERM:00063 the study of the network of interactions between proteins, metabolites and other biological objects in the cell, and the consequences of those interactions JERM:00129 JERM:00030 JERM:00099 Mass spectrometry (MS) is an analytical technique for the determination of the elemental composition of a sample or molecule. It is used for elucidating the chemical structures of peptides and sometimes other chemical compounds JERM:00103 JERM:00052 JERM:00054 JERM:00067 JERM:00065 JERM:00071 quantitative metabolomics JERM:00091 JERM:00133 JERM:00092 JERM:00100 JERM:00101 techniques for labelling molecules to allow them to be detected in laboratory analyses JERM:00034 JERM:00029 JERM:00035 JERM:00074 JERM:00062 JERM:00118 JERM:00075 JERM:00064 JERM:00076 JERM:00077 JERM:00078 JERM:00079 JERM:00072 Proteomics is the study of the function and structure of proteins in an organism, predominantly using high-throughput techniques JERM:00104 also known as real-time PCR or quantative PCR quantitative real time polymerase chain reaction (Q-PCR/qPCR) or kinetic polymerase chain reaction, is based on PCR and is used to amplify and simultaneously quantify a targeted DNA molecule JERM:00105 Real-time reverse-transcription PCR, qRT-PCR Reverse transcription polymerase chain reaction (RT-PCR) is a variant of polymerase chain reaction (PCR). In RT-PCR an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR. JERM:00136 JERM:00080 the study of biochemical reactions in the cell JERM:00053 JERM:00084 analysing the response of single cells to stimuli and perturbations by fluorescence and imaging JERM:00082 JERM:00134 JERM:00032 JERM:00102 JERM:00107 JERM:00036 JERM:00092 JERM:00085 The study of the transcriptome, the complete set of RNA transcripts produced by the genome at any one time JERM:00089 also called cDNA Microarray JERM:00055 JERM:00090