Areas

Areas

Overview

In PlateEditor, layouts are created by assigning Areas to the wells of your plate. An Area can represent anything that need to go inside the well: any sample, compound, cell line, bacterial strain, enzyme, antibody, etc...
However, there is no need to create a distinct area for each concentration, multiplicity of infection (MOI) or combination related to your sample: this is done by overlapping areas on different layers and adding concentration data separately (see below for examples and more details).
Areas can be created and edited using the controls available under the Areas group of the [Menu Panel]. An Area is defined by few simple properties: a name, a color and a type.

Area name
Each area must be attributed a unique name of at least 3 characters. When creating or editing an Area, an error message will signal the user if the chosen name is too small, or already used.
Although there are no restrictions in the maximum number of characters for the name of an area, it is recommended to use concise names, briefly but precisely describing the object to add to the well.

Area color
Areas will be depicted using their colors on the plate layout. A color will automatically be proposed by PlateEditor when creating a new area, but any color among a list of 138 can be used.
Although different areas can be assigned identical colors, it is recommended to select different colors for each, in order to differentiate them more easily on the layout.

Area type
There are currently 4 types of areas in PlateEditor: Sample, Positive Controls, Negative Controls and Ranges. Here is the description of these types:
- Sample: this type is the most generic and is used to describe anything that fits into a well.
- Positive/Negative Controls: these two types are used to indicate that the well contains a reference compound, inhibitor, solvent or anything that will be used as control in the experiment. Values for the wells tagged as Controls will be available for aggregation by the Controls Report tool (see [Analysis] page). There are also restrictions applying preventing the overlap of Controls with Sample (or Ranges) while in Strict Mode. See [Tagging] for more information.
- Ranges are specifically designed to handle repetitive lists of Samples. They possess self-incrementing features and can be attached to Definition files for the resolution of each index. See the [Ranges] page for more information.

Creation of area

This is done through the form (1) illustrated above, accessible from the New/Edit buttons under the Areas group of the [Menu Panel].
When clicking on the color control (1a), a new form will open, allowing selection of another color from the proposed list (2). Click on the desired color to update the color selected (2a), and click OK to apply it to the area.
The type of the area can be selected from a drop-down list (1b). Additional options will show for ranges, see the [Ranges] page for more information.

Examples

Here are some expamples to better understand the areas and how to choose the correct type for what you are trying to do.

The combination nightmare
Let's consider an experiment whose aim si to investigate the celullar responses of various cell lines to different pathogens. There will be 3 different cell lines (1 from human, 2 from mice) to assess with 3 pathogens (a wild-type (WT), a deletion mutant, and its complement).
Of course we would like to test different multiplicity of infection (MOI) for each pathogen, at least 3 (low, medium, high) and do every conditions in multiple replicates.
Summing things all up, we end up with 3 cells × 3 mutants × 3 MOI = 27 unique samples. Since we work in 384-well plate, we can set the replicates to 8 to maximize the space used on the plate and the statistical strength. There will still be free spaces on the side of the plate, to limit the edge-effects.
If you were to make the layout for this experiment using Excel, you would probably end up with something like this:

To simplify the problem, the plate is usually represented as a three-entry table, with the cells, pathogens and MOI information each forming a distinct entry. It would indeed be a pain to indicate the full name of the sample everywhere it applies, for instance Cell A + WT MOI 1, Cell B + Mutant MOI 5, etc... And this for all the 27 samples!
The same principle applies in PlateEditor: there is no need to define all 27 samples. The individual cell lines and mutants will be defined as Sample typed Areas. MOI will be defined separately as well, as concentrations.
To indicate to PlateEditor that several samples are together in the same well, we will use Layers. Here, 2 layers are needed: one for the cell lines, one for the pathogens, and The MOI data can be added to the pathogen layer.
In summary, the areas defined and the final layout would look like this in PlateEditor:

Primary screening
Here, we would like to perform the screening of a small library of compounds, let's say 500, using an assay running in 96-well plates. As for all good screening, each plate will have internal controls, which can be added in the first and last columns (of course we verified there were no edge-effects for this assay).
The remaining wells (80) will be for the compounds, each tested in single dose (5 μM) and the whole thing done in duplicates for more statistical power.
All-in-one, there will be 6 plates full and 1 plate with only 20 compounds, for a total of 7 unique plate layouts.
We don't want to make 7 different layouts, each containing 80 different areas of type Sample. Hopefully, we won't have to, because we can use a single Range instead.
Ranges are specifically designed for repetitive sequences of samples, and can be anchored with definition files to handle the name resolution automatically. See the [Ranges] page for more information.
Here, the entire set of plates is defined by only one layout containing 3 areas: a positive and negative control, and a range with 1 replicate, as shown below.

The problem is then reduced to the generation of a correct definition file for the screening, which is not going to be a big issue since we have the compound library information, as listed by the supplier. For more information about this aspect, see the [Ranges] and [Definitions] pages.
Additionally, as we defined positive and negative controls in the plate, we can access the functionalities offered by the Controls analysis tool, allowing computation of the Z' and window for each result plate. See the [Analysis] page to learn more about this tool.