Introduction to the Biomaterial collection

The Biomaterial (Samples) section contains collections of different sample types. It can be regarded as another lab collection category; indeed, the features and behavior described in the previous section are also available on the Biomaterials category. However, the biomaterial collection also offer an extended set of features.

The Biomaterial category offers a default Sample suitable for most situations. More specialized biomaterial types like Sequencing Library can be created to cope with specific assays (i.e. an Illumina Sequencing assay) and have, on top of the base Sample's attributes, specific properties to record information about the sequencing. This information is required when submitting data to public repositories.

In LabID, an assay consumes samples to generate datasets by mean of a specific instrument e.g. a sequencing assay consumes sequencing libraries to generate fastq datasets by mean of a sequencer. Learn more about these concepts

Sample Types

Several sample types are made available. The base sample is named Generic . Certain experiments/assay types require to capture additional intrinsic sample properties to be able to be fully reproducible. To accommodate more complex cases, specialised sample types and flags were implemented.

• The following sample types are currently supported

  • Generic sample

  • Sequencing library

When registering datasets obtained from running an assay, it is necessary to pick the adequate sample type as certain assay type can only be successfully registered using the proper sample type (currently this is only the case for sequencing, where sequencing assays will only accept sequencing libraries)

• The following sample flags are currently supported

  • Control flag, for control sample

  • Single-cell flag, for single-cell sample

  • Screen plate position flag, for sample on a plate

What sample type should I use ?

• The sample type is generally dependent on the assay type.
• One can always start with a generic sample and specialise it over time, however this is needed only when you want to (1) register your sample prior to dataset registration, (2) re-use samples existing in the system. Indeed, when registering an assay, samples can be auto-created

The Generic sample type is the base model. When no specialised sample is needed, this is the one to start with.

Flags

Control sample flag

When a positive or negative control is needed in a study, a control sample can be created. Control samples can be flagged as so, which will display control specific properties (e.g. control type)

Single-cell sample flag

Specific single-cell attributes can be described when a sample is flagged as a Single Cell sample

Support for plate-based screen

A plate position (plate name, type & well) can be described for every sample flagged as Screen plate position . This is particularly useful when samples are handled by robotics during a e.g. plate-based screen. Technical replicates can be distinguished by their different positions on the plate.