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3 | Adding samples to your order

Add and organize your samples and plates, assign tests, define controls, and finalize your order before sending it to the lab.

Written by An Broekmans
Updated over a week ago

Once your order is created, the next step is to add samples/sample bags and assign tests. This is where you define the biological material that will be analyzed, organize them into plates, and optionally add controls. When everything is ready, you mark the order as shipped to hand it off to the lab.

Sampling method: Sample plates

Sampling method: Sample bags

After you've selected one of these options, all other options are still available. You can still use the actions menu to use import/export options:

Export Kraken XML functionality is only available for laboratories.

The screen and actions will automatically adjust in case the requested order type requires sample bags instead of sample plates.

Adding samples individually

Perfect for small or simple orders, this option lets you click into individual wells and enter sample names manually. You can:

  • Name each sample freely, add them to a(n existing) plate

  • Add tests one by one or in bulk depending on the order type setting for flexibility to add tests on order, plate or sample level.

This is great for quick jobs or when plates aren’t completely filled.

From the table, you can tab (and shift-tab) much like you would manage a spreadsheet. You can assign all the tests assigned to the specific crop/variety and order. You can create a new plate by typing a new plate name or add the sample to an existing plate by typing the same name. Optionally, you can add a plant name, number and plot.

Import plates without samples

This workflow is typical for bulk, plate-based orders that are anonymously uploaded into Lab Portal (for instance: a purity order for 50 plates, each representing a bag of seeds).

In this modal, you can rapidly generate plates and samples. Here's how it works:

  1. Define the amount of reserved positions (typically negative template controls) and how they need to be positioned

    1. Column-oriented, first X positions (always as first x positions)

    2. Column-oriented, last X positions (always as last x positions)

    3. Column-oriented, after last sample (immediately after the last sample)

    4. Row-oriented, first X positions (always as first x positions)

    5. Row-oriented, last X positions (always as last x positions)

    6. Row-oriented, after last sample (immediately after the last sample)

  2. Choose a sample ID generation method

    1. Plate + Well position (e.g. {{PlateName}}-A1)

    2. Plate + Number (e.g. {{PlateName}}-001)

  3. Type in (or copy paste from a CSV/ spreadsheet) your plate names

  4. Choose Marker/target assignment per plate, or the same for all plates

Once you've done this, you can still edit the details of anything on your plate, or start over by deleting (a selection) of your samples.

Bulk import samples

In case you're working with bigger imports, you can also choose to upload a CSV file. An example with all the possible fields is available right from the samples start screen:

The file will contain all the possible values, but for a full technical specification of the file, read below information:

Sample CSV specification

This file can be prepared manually, edited in Excel or Google Sheets, or downloaded and modified directly from the application.

Format Overview

The system expects a column-based csv file

Column Definitions

Field Name

Required column

Description

SampleName/SampleBagName

Yes

Unique identifier for the sample/sample bag. This is the only required field.

PlantName

Yes

Optional identifier, often used for plot/plant combinations

MasterPlateName

Yes

Name of the plate to place the sample on.

MasterPlateWell

Yes

Specific well position on the plate (e.g. A1, H12).

Plot

No

Plot ID (can be used with plant number to structure names)

PlantNumber

No

Plant number within the plot

Sample bag Columns

Optional Sample bag information can be added to the import csv file in case the order type allows this input.

Field Name

Required column

Description

Subsampling

No

Amount of subsampling defined by the laboratory. Available as a dropdown list when entered manually.

Quantity

No

Min and max quantities defined by the laboratory

Unit

No

Possible units defined by the laboratory. Available as a dropdown list when entered manually.

An error message pops up in case the imported information was not as expected/configured for that order type.

Test Columns

Each column should be named after a test in your test catalog. Accepted values (all case insensitive) in test columns:

Value

Meaning

1, Y, YES

Test is assigned to the sample

0, N, NO

Test is not assigned

(blank)

Test is not assigned (default)

Behavior Notes

  • The first 4 column headers are obliged to be available. Optional, 2 additional columns (Plot & PlantNumber) can be added. The order of each column is not important.

  • Plate and Well are optional. If they are missing, you can still add them in the Samples view (via actions in a semi-automated way)

  • The sample name must be unique within the order. If a sample with the same name already exists, uploading a CSV with that name will update the existing sample.

  • You can download a current CSV of your samples at any time, make changes in a spreadsheet tool, and re-upload it.

  • Test names must exist in your test catalog. If a column header doesn't match a known test, this will be ignored

  • Via Settings > Integrations: you can configure samples ID's to be ignored during import. eg 'Empty'

Changing status to 'Shipped'

Now that you've added samples to your order, you can add a tracking URL to ship the orders to the laboratory.

In this article, we'll explore how you can process orders in more detail.

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