Conditions that have been established to measure effects which are induced in cells in response to a perturbation, together with data that have been acquired in these measurements in order to address the biological question this project was designed for. Contact details of researcher/person/laboratory/institution in charge of the project Description of biological process that is addressed and description of measured effect. Description of the specific application of this project within a larger context, if applicable. Array supports (reaction vessels where perturbations are carried out) that are used during the project Description of the materials that are utilized in the project. Cells used during the assay. Description of reagents (media, supplements, transfection reagents) used during the assay with: Name, manufacturer, order number, type (e. g. 'medium', 'antibiotic', etc.). Also perturbators, like siRNA, small chemical compound, expression construct are reagents. If they are part of a library, then this library needs to be described as well. Mapping to individual perturbators (e.g. siRNAs in a library) is done with a link to a mapping file (e.g. plate numbers and XY coordinates). The connection of an individual perturbator to a particular array position may be established in the process line. Media used for the cell-culture(s) during the project. Description of the instruments required for the assay, e.g. data acquisition station. Detailed descriptions of such instruments and their settings could be part of spezialized documents or be given in Treatment, Post-Treatment, or Data Acquisition. Instrument name Instrument type, e.g. liquid handling robot, centrifuge, FACS, Plate Reader, etc. Contact details of the instrument manufacturer. Instrument Model e.g. objective lenses, numerical aperture, filters The actual experimental part decribing the performed steps, like treatments, perturbation(s) and data acquisition in necessary detail. Description of the conditions that are applied to CellLine during culturing of cells. ‘Treatment’ also covers the perturbation. More than one perturbator can be applied in the same ‘Treatment’. Description of the conditions, i.e. lysis, fixation, staining, antibody incubation, etc., that may be applied after ‘Treatment’, and prior to data acquisition Detection of the effect(s) induced by the perturbation Description of the processes applied to analyze the raw-data in order to generate a hit list. Data analysis is usually carried out sequentially, applying a number of algorithms and analysis tools Description of raw data. number, image, movie,… ASCII, TIFF, WMA,… link to raw data The raw data can be processed either manually or through automated computational methods. Processing commonly generates numbers and/or phenotypic descriptions. reference to a publication number, image, movie,… ASCII, TIFF, WMA,… link to raw data A phenotypic description is usually obtained by manual observation of images and/or interpretation of processed data. for the characterization and classification of phenotypic observation description of phenotype Time and Space parameters number, image, movie,… ASCII, TIFF, WMA,… link to raw data The experiment workflow a Treatment, Post-Treatment or DataAcquisition Step e.g. cell propagation, siRNA transfection ID of the referenced step ID of a successor element of the process step Used to descibe the contact details of the scientist name of the researcher working on the project. name of the institution/affiliation the researcher is working at department in the institution address of the institution city the institution is placed country the city is placed email of the researcher Description (text) of the process within a larger context Application title, e. g. as taken from a publication biological process that is addressed description of measured effect and the 'reporter' used for the measurement (e.g. antibody) controls are relevant in data analysis to determine the robustness and the dynamic range of the assay, and to produce the list of significant hits. Refers to the term of the controlled vocabulary in an external database. controls are relevant in data analysis to determine the robustness and the dynamic range of the assay, and to produce the list of significant hits. Application abstract, e. g. as taken from a publication reference to publication Bibliographic reference for the data generated during the project. Cross reference for the data source. Example: Entry in a database of databases. Crossreference to an external database. Crossreferences to literature databases, e.g. PubMed, should not be put into this structure, but into the bibRef element where possible. Primary reference to an external database. Further external objects describing the object. Refers to a unique object in an external database. Name of the external database. Taken from the controlled vocabulary of databases. Accession number of the database in the database CV. This element is controlled by the PSI-MI controlled vocabulary "database citation", root term ID MI:0444. Primary Identifier of the object in the external database, e.g. UniProt accession number. Secondary Identifier of the object in the external database, e.g. UniProt ID. The version number of the object in the external database. Reference type, e.g. "Identity" if this reference referes to an Identical object in the external database, or "see-also" for additional information. Controlled by CV. Reference type accession number from the CV of reference types. This element is controlled by the PSI-MI controlled vocabulary "xref type", root term ID MI:0353. Description of array support types (reaction vessels) that are used during the project: i.e. single eppendorf tube, 96-well plazes, or [glass] slides, with details such as manufacturer, order number; size. Type of vessel used,: i.e. single eppendorf tube, 96-well plate, etc. Size of reaction vessel, e.g. volume or surface area. details respective to size surface area in mm² number of wells Contact details of the source of the reaction vessels, e.g. company Cell line used during the project. Description of the cell line used. (e.g. HeLa ATTC CCL2) information about the cellLine if not ATCC details of the cellLine in case no ATCC No. is rendered e.g. ATCC controlled vocabulary ID e.g. human e.g. kidney e.g. totipotent stem cell (CL:0000723) a variant of a cellType is a collection of interconnected cells that perform a similar function within an organism reference to publication contact details refering to the CellLine is the generationNo of a CellLine due to passaging and growing transgene/genetic manipulations, e.g. stably transfected, induced resistance measures undertaken to validate cell line, e.g. DNA fingerprinting, genotyping, morphology testing Mycoplasma test (Y/N) and other measures for quality control, e.g. virus testing controlled vocabulary for celltypes ID of cell.obo name derived from other ontologyID Allows to reference an external controlled vocabulary, or to directly include a value if no suitable external definition is available. This contains the controlled vocabulary terms Refers to the term of the controlled vocabulary in an external database. Composite Reagent name of cell culture medium comment One or more reagents in a cell culture medium References to the production of the composite reagent for subsequent application Temperature at formation e.g. incubation of siRNA with transfection reagent prior to transfection composite reagent reference to protocol description of array type and array support type/vessel One or more reagents in a composite reagent, e.g., a cell culture medium Reference to ID of a reagent Volume/amount of the reagent in the composite reagent e.g. mL, g concentration of the reagent in the composite reagent e.g. mol/L details on the reagentType reagent name, e.g. name of a gene / cDNA, water, FBS reagent type, e. g. cDNA, small molecule, siRNA. If available, reference to a controlled vocabulary. e.g., sequence of siRNA; structure/ChEBI for compound Details to the vendor or manufacturer Target Species e.g. if siRNA e.g. geneID of target gene in case of siRNA stock concentration e.g. mol/L Solvent e.g., transfection/transduction efficiency of 'cell type' (average, cv) with ‘Perturbator’ (library) description of array type and array support type/vessel details on the library the perturbator is part of details if perturbator is virus details if perturbator is chem. compound % of compounds with >80% purity % of compound comply with Lipinski rule-of-5 Average molecular weight if perturbator ist part of a library name of the library library ID as a reference Type of library: (gain-of-function/overexpression (cDNA, ORF, other); loss of function (siRNA, shRNA, miRNA, viral, other); compound; other reference on library (if available) single/pooled - e.g. shRNA pool Details to the vendor or manufacturer Preparation methodology number of unique features (e.g. genes, compounds) represented in library, reference to where a list of these features can be found PlateNumber and well position; mapping of individual perturbators in library format. LibraryFeatures of perturbators (length of siRNA/shRNA, type of hairpin, other). Description of the conditions that are applied to CellLine during culturing of cells. ‘Treatment* also covers the perturbation. More than one perturbator can be applied in the same ‘Treatment’. description of array type and vessel e.g. mL e.g. mol/L e.g. mL e.g. mol/L e.g. °C e.g. % e.g. % e.g. hours Detection of the effect(s) induced by the perturbation Reference to the instrument-settings e.g. seconds reference to a protocol/publication description of array type and vessel reference to a vesseltype column row number of feature/well if explicit Details to the vendor or manufacturer name of the company OrderNr SerialNr LotNr