CASSbase: link vector controls and transgenic lines

[MercedesThieme]

For each transformation batch (creation of different transformed lines), multiple vector control lines containing an empty vector are generated. Those function as controls for all the transgenic lines generated in the same batch.

Feature request: It would be great if this information (who belongs to whom) could be seen on the accession page. It could be similar to the pedigree section but with the difference of many-to-many connections (all transgenic plants of the batch belong to all vector control lines of the batch). In the future, this information could directly come from the Transformation Tracking tool, as they are all (transgenic lines & vector controls) connected by the transformation date. However, a batch upload for the already implemented accessions would be needed (again, similar to the pedigree upload via excel).

[titima15]

@MercedesThieme For the "vector controls", do you mean "vector constructs"?

[lukasmueller]

No these are transformations without any vector as a negative control.

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[titima15]

Actually, based on the first statement, it will be empty vector (a vector without gene of interest).

[MercedesThieme]

A vector control is a plant that has been transformed with an empty vector. In this process, the plasmid, including antibiotic resistance markers, is introduced into the plant, but it does not contain any gene of interest. This type of control is advantageous compared to a wild-type control because the vector control plant undergoes the same "stressful" transformation process as the test plants. However, it should not exhibit any effects attributed to the gene of interest present in the transformed plants being compared.

Vector controls are created during the same transformation process as the transgenic plants. This means that a single vector control plant serves as a control for all the plants that were transformed in the same batch (ie on the same transformation date)(eg. VC_FAU353 is a vector control plant for all lines of C2-37 and C2-48, as they were all transformed on the same day).

In each batch, multiple lines are generated, which applies to both the transgenic plants and the controls. Therefore, each transgenic line has multiple vector control lines (eg line C2-37_FAUxxx has 20 vector control lines VC_FAU342 to VC_FAU361).

This creates a many-to-many relationship between transgenic lines and vector controls. It would be great to display this relationship on the accession page, either in a pedigree style or as a list. Additionally, displaying the co-culture date (or transformation date) on the accession page would be good.