Cell Lines

In vitro experiments (e.g., cell lines) allow manipulate tumor cells in a controlled, artificial environment and testing the effects of different drug therapies. The LAS system defines a Cell Line as the set of bioentities that are generated from the same source and are under the same experimental conditions. The experimental conditions are defined by the protocols that describe the type of process (i.e., adherent, suspend, organoid) and the set of culturing conditions applied. The culturing conditions are defined by a set of items categorized in the following groups: (i) Nutrients and chemical, (ii) Hormones/growth factors, (iii) Antibiotics, (iv) Serum, and (v) Media. The Cell Line Management Module aims at tracking the life cycle of cell lines and monitor the experimental conditions applied to each cell. The main functionalities provided by this module include the following.

Protocol Manager

To manage properly Cell Line entities the user should define protocols for both generation and expansion procedures. Each protocol defines on which procedures can be applied (i.e., generation or expansion) and the type of process (i.e., adherent, suspend, organoid) exploited on cell lines. The system requires an unique name for each protocol. Moreover, the users can describes the items (i.e., culturing conditions) used by the protocols in manipulating the cell lines. The culturing conditions are categorized in the following groups: (i) Nutrients and chemical, (ii) Hormones/growth factors, (iii) Antibiotics, (iv) Serum, and (v) Media. The user can select one or more culturing conditions and define, where it is required, associated parameters (e.g., concentration, dosage).

Generation

Cell Lines entities can be generated only form viable aliquots. In this procedure, the user can generate new cell lines by selecting one or more generation protocol. The system automatically generates the new Cell Line entities according to the information of selected protocols. The user can schedule a cell line generation for a set of aliquots from the Biobank module. This set of aliquots is visualized in the “Pending Generation” page. The user can also generate aliquots without a schedule using the interface “New Generation”. In both pages, the user should select the generation protocols of interest and then select the aliquots form which she wants generate new Cell Lines. In the New Generation page, similarly to the implantation of xenografts, the viable aliquots can be loaded by means of the container barcode.

Expansion

The user can visualize and manage the currently available cell lines owned by her WGs. The user can perform a set of operations on each cell line: (i) trash one or more plates, (ii) expand the cell line by defining dilution parameters, expansion protocols and the number of output plates for each protocol, (iii) send a set of plates to experiments (fake viable aliquots are created in the Biobank), and (iv) plan an archive procedure. It is possible to filter the list of shown cell lines according to their GenealogyID or the last user who manipulated the lines.

Archive

In the expansion interface the user can schedule one or more cell lines for the archive procedure. All the scheduled cells are listed in the archive page. For each cell line the user can archive different aliquots types with their associated parameters (e.g., volume [ml], count [cell/ml]) and position them in the destination container.

Thawing

Similar to the generation procedure, the user can create new cell lines from the viable aliquots generated from archived cell lines. The user can schedule a cell line thawing for a set of aliquots from the Biobank module and then process them from the “Pending Thawing” interface. Differently, she can load containers by means of their barcode and select the target aliquots from the “New Thawing” page. In both cases, the user should select the generation protocols exploited for the operation and then select the aliquots form which she wants generate new Cell Lines.