When submitting data to the IDR, you should provide 3 basic files:
All files should be in tab-delimited text format. Templates are provided but can be modified to suit your experiment. Add or remove columns from the templates as necessary. The templates can be opened in Excel, Open Office etc.
This file should contain a general description of the study, and then list the screen(s) performed, along with the protocols describing how each screen was set up, imaged and the data analyzed, including the criteria used to identify genes of interest.
For each screen the following information should be included:
If there is more than one screen in the study, then copy and past the previous ‘screen block' of text so it can be filled in again for the next screen.
Each screen should have a library file describing the plates and the cells in each well. Columns can be added or removed as appropriate but this file should include:
The Reagent Gene Annotation Build refers to the gene annotation build used to design the reagent e.g. siRNA. The Analysis Gene Annotation Build refers to the gene annotation build used in the current analysis. Sometimes this is the same, in other cases the reagents have been remapped to a more recent build. The gene annotation build should contain both the genome build and gene build if possible e.g. “GRCh37, Ensembl release 61, Feb 2011” or “NCBI36.3, RefSeq release 27, Jan 2008”.
Each screen should have a processed data file that contains summary information about the results found. This may be a table from the associated publication. This file can contain information relating to each well in a screen e.g. the total number of cells and number of tagged protein foci, or be a list of genes found to show significant phenotypes.
The information in the processed data should be linkable to the library file in some way e.g. by combination of plate and well, or by identifiers such as siRNA or gene identifiers
The contents of each column in the processed file should be described in the study file so that is clear what the values are.
Lists of terms that can be used in the study and library file can be found in this google doc.
Example files can be found in https://github.com/IDR/idr-metadata. If you are not familiar with github, it is a way of storing versions of files. You can browse the files through the github interface. If you want to download a file you can click on the ‘Raw' button on the top right hand side above the file preview and then do File -> Save Page As in your browser, or if you are familiar with github you can clone the repository. There are files in addition to the study, library and processed files in the repository but you don't need to provide these.
Examples of HCS studies include:
Email firstname.lastname@example.org with any questions.
© 2016-2021 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 4.0 International License.
OMERO is distributed under the terms of the GNU GPL. For more information, visit openmicroscopy.org