Samples result from processing events applied to biosource material or other samples before they are turned into an extract. In other words, samples can be created from biosource items or from one or more sample items. When a sample is created from several other samples, a pooling event is performed.
For every step of transformation from biosource to sample, it is possible to provide information about the protocol used to perform this task. It is not enforced in BASE but it should serve as guidance when devising the granularity of the sample processing task. Also, it is good practice to provide protocol information to ensure MIAME compliance.
Use → to get to the list of samples.
Beside the common way, using the button, a sample can be created in one of the following ways:
- from either biosource list- or single view- page.
No matter how complex the sample processing phase is, at least one sample has to be anchored to a biosource. Therefore, a natural way to create an sample is to click on
in the sample column of the biosource list view. There is also a
corresponding button,
in the toolbar when viewing a single biosource.
- from the sample list page
Pooled samples can also be created by first selecting the parents from the list of samples and then press in the toolbar.
- Name
The sample's name(required). BASE by default assigns names to samples (by suffixing
s#when creating a sample from an existing biosource orNew Sampleotherwise) but it is possible to edit at will.- External ID
An identification used to identify the sample outside BASE.
- Original quantity
This is meant to report information about the actual mass of sample created.
- Created
A date when the sample was created. The information can be important when running quality controls on data and account for potential confounding factor (e.g. day effect).
- Registered
The date at which the sample was entered in BASE.
- Protocol
The protocol used to produce this sample.
- Bioplate
The bioplate where this sample is located.
- Biowell
Biowell that holds this sample. Bioplate has to be defined before biowell can be selected.
- Description
A text field to report any information that not can be captured otherwise.
This is meant to keep track of the sample origin. BASE distinguished between two cases which are controlled by the Pooled radio-button in the edit pop-up window.
If the parent is a biosource the radio-button is set to No . This will make the biosource select button active, which allows users to point to a biosource from which the sample originates from.
When the parent is one or several other samples the radio-button is set to Yes . Upon selection, the biosource select button is deactivated and the samples box and button are activated. This allows users to specify one or more samples to be selected from a sample list view page.
As seen in the biosource section, this tab allows users to further supply information about the sample provided they have defined or shared annotation types to annotate sample items.
To learn more about annotation types and how to define a value for a type, please refer to Chapter 11, Annotations
This tab contains a list of those annotations that are inherited from the sample's parents. Information about working with inherited annotations can be found in Section 11.4.1, “Inheriting annotations from other items” .