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 experiments(s) performed, along with the protocols describing how each experiment was set up, imaged and the data analyzed.
For each experiment the following information should be included:
If there is more than one experiment in the study, then copy and past the previous ‘experiment block' of text so it can be filled in again for the next experiment.
Each experiment should have an assay file describing the samples and the images of them. In this file, each image should have its own row, and it is almost like a time line, with the starting sample described first (left hand side of the row) and then moving through treatments to the sample (referencing the protocol names described in study file), then the imaging assay, then the data analysis and finally listing the file with the results in it. In more detail, working from left to right the row for each image should contain:
Each experiment 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 image or be values calculated from several images.
The information in the processed data should be linkable to the assay file in some way e.g. dataset name
The contents of each column in the processed file should be described in the study file so that it 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 non-screen studies include:
Email email@example.com with any questions.
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