Sample Types¶

A single sample model is not suitable to accurately describe the specificities of different experimental conditions and procedures. In other words, different intrinsic sample metadata needs to be captured whether you are performing a sequencing assay or an imaging assay. To accomodate the most commonly performed analyses, we have developped mutliple sample types.

LabID supports multiple platform & technologies

The Data Management section of this Getting Started guide presents how LabID has been designed to support multiple platform and technologies. In addition of different sample types, which we focus on in in the present section, LabID also - out-of-the-box - provides multiple assay types to precisely describe data acquisition procedures.

Sample Types¶

A base sample type¶

The Biomaterial category offers a default sample type - simply called Sample - suitable for situations where there is no specialised sample type to be used.

Specialised sample types should always be used when available.

The base sample type is only made available to accomodate cases where no better sample type exists in LabID. In case a more specialised sample type exists and fits your use case, it should always be used.

Specialised sample types¶

Specialised sample types have been developed to record process specific information. On top of the base Sample attributes, specialised sample models have additional sets of properties to record domain-specific information. For example, unlike an electron microscopy sample, a sequencing library has a sequence barcode. This specialised information is essential to understand how a sample was obtained, and usually to understand the downstream data, and is therefore required when submitting this data to public repositories.

The following specialised sample types are currently available:

Sequencing library (for Nanopore and Illumina Sequencing assays)
EM sample (for Transmission and Volume Electron Microscopy assays)

What sample type should I use ?

As mentionned above, specialised sample types should always be used when available. The type of sample to be used is generally governed by the assay type. When loading data as part of an assay, LabID is able to auto-create the samples of the adequate type.

Sequencing assays

Sequencing Library
Light Microscopy (LM) assays

Base sample
Electron Microscopy (EM) assays

Electron Microscopy (EM) Sample

However, it is also possible to create your samples prior to dataset registration. This is useful, for example, to be able to cross reference these samples in your electronic lab notebook. When unsure about the final sample type - or when the same parent sample will be used to perform different kind of assays -, we advise to start from a generic sample and specialise it as needed.

Generate a generic sample.
Generate a specialised descendant sample (i.e. derive a specialised sample from a generic parent sample)

When appropriately creating a child sample, LabID keeps track of its parent.

Samples may also already exists and/or need to be specialised when they re-used in follow-up experiments.

Sample Flags¶

In addition to different sample types, each sample model in LabID has a set of boolean flags. When a given flag is set to true, additional flag-related information needs to be recorded.

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

Control sample flag¶

Control samples need to store information about the:

Control name
Control type (e.g. positive/negative control, etc.)

Single-cell sample flag¶

Single-cell sample need to store information about the:

Cell type
Cell number

Plate-based screening sample flag¶

Plate based samples used in screening need to store information about the:

Plate name
Plate type
Plate position
Plate code

Technical replicates can be distinguished by their different positions on the plate.