ChIP target(s) --> Submissions

This template can be used to search for all submissions (submission is an instance of an experiment e.g. one of the biological replicates in a ChIP-chip experiment) that have used the specified antibody(s). As an input, an antibody (ChIP Target) or a list of antibodies (ChIP targets) can be used to query toxoMine. Example shown below: a user can quickly find all ChIP-chip submissions that targeted GCN5b binding sites.

Experiment(s) --> Sequence features

This template can be used to query for the sequence features, e.g. histone binding sites, for the specified experiment(s). Instead of finding sequence features per submission (submission is an instance of an experiment e.g. one of the biological replicates in a ChIP-chip experiment), users can use this template to find all available sequence features for the specified experiment(s). If there are multiple submissions belonging to the specified experiment(s), this will return all sequence features found in those submissions as one table. As an input, name of an experiment or a list of experiment names can be used to query toxoMine.

Experiment category(s) --> Submissions

This template can be used to search for all experiments (thus all subsequent submissions - submission is an instance of an experiment e.g. one of the biological replicates in a ChIP-chip experiment) that fall into the specified experiment category(s). As an input, name of an experiment category or a list of experiment category names can be used to query toxoMine.

Experiment category(s) --> Toxoplasma mutants

This template can be used to search for all experiments (plus toxoplasma mutants used for that particular experiment) that fall into the specified experiment category(s). As an input, name of an experiment category or a list of experiment category names can be used to query toxoMine.

Feature type(s) --> Submissions

This template can be used to query for all submissions (submission is an instance of an experiment e.g. one of the biological replicates in a ChIP-chip experiment) which produced the specified sequence feature(s), e.g. histone binding sites. As an input, name of an sequence ontology term or a list of sequence ontology terms can be used to query toxoMine.

Project(s) --> Sequence features

This template can be used to query for the sequence features, e.g. histone binding sites, for the specified project(s). If there are multiple experiments and multiple submissions belonging to the specified project(s), this will return all sequence features found in those experiments and submissions as one table. As an input, name of a project or a list of project names can be used to query toxoMine.

Protocol type(s) --> Submissions

This template can be used to query for all submissions that utilized the specified protocol type(s). As an input, name of a protocol type or a list of protocol type names can be used to query toxoMine.

Submission(s) --> Sequence features

This template can be used to query for the sequence features, e.g. histone binding sites, for the specified submission(s). As an input, name of a submission or a list of submission names can be used to query toxoMine.

Submission(s) + Submission(s) --> Binding sites

This template can be used to query for the overlapping binding sites between submissions (submission is an instance of an experiment e.g. one of the biological replicates in a ChIP-chip experiment). As an input, name of a submission or a list of submission names can be used to query toxoMine. For example, users can quickly compare if there are overlapping binding sites between two ChIP-chip submissions that targets the same gene but are derived from two distinct sources.