Sample Batch

Definition

A sample batch forms a logical container of samples that are going to be shipped together to the measurement facility with the intention of being processed under the same conditions.

Intention

Grouping and processing samples as distinct sample batches is key in properly tracking and avoiding batch effects. Click here for a quick introduction into batch effect and their impact on research data.

Creating and registering sample batches

We call the process of adding samples to an experiment "sample registration". When you want to link samples to an experiment you need to register metadata for those samples.

To start with the sample registration process, click on the button Register sample batch to open the sample registration dialog.

Please go ahead and download the metadata template file from the dialog. In this file you can fill out information for the samples you want to register.

Note

Mandatory information for the sample registration is marked by an asterix * after the column name.

Once you filled out all the information, you can go back to the dialog. In case you closed the dialog, simply re-open it.
Please go ahead and upload your filled metadata file in the dialog. Once the data manager validated the information in your file, go ahead and choose a name for your batch.
Once you named your batch and uploaded the file with the necessary information, go ahead and click the Register button. The data manager will now go through the process of creating samples within your experiment.

Email Notification

Upon successful batch registration, all project collaborators will automatically receive an email with a link to the created batch.

After the data manager is done registering your samples, you can close the dialog by clicking the Finish button. Now samples annotated with the provided metadata are registered to your experiment. You can see the newly created batch next to the other batches in the samples view.

SampleId

Upon successful batch registration, each sample will be associated with a unique SampleId distinguishing it from other samples within the system an email with a link to the created batch.

Editing sample batches

You might need to edit sample metadata after registering the sample batch to the experiment. Editing sample information is restricted to editing the sample metadata. Adding or removing samples from a batch is not possible.

To start with the sample edit process, click on the edit button next to the batch you want to edit. This will open the batch editing dialog.

Project role

Should you not see the action column,
please make sure that you have been granted the "write" or "admin" role to it by the project owner/admin.

Please go ahead and download the metadata template file from the dialog. In this file you can fill out information for the samples you want to register.

Note

Mandatory information for the sample editing is marked by an asterix * after the column name.

Note that the information in greyed out columns such as e.g. Sample Id is immutable and changes made within will not be registered during the sample editing process.

Note

Information shown in greyed out columns are immutable and cannot be changed.

Once you filled out all the information, you can go back to the dialog. In case you closed the dialog, simply re-open it.
Please go ahead and upload your filled metadata file in the dialog. Once the data manager validated the information in your file, go ahead and choose a name for your batch if you want to change it.
Once you named your batch and uploaded the file with the necessary information, go ahead and click the Edit batch button. The data manager will now go through the process of updating the sample information within your experiment.

After the data manager is done registering your samples, you can close the dialog by clicking the Finish button.

Delete a sample batch

Batch Deletion

Keep in mind, that deleting a batch will also delete all sample metadata of the samples within the batch

To start with the sample batch deletion process, click on the delete button next to the batch in question within the action column.

Project role

Should you not see the action column,
please make sure that you have been granted the "write" or "admin" role to it by the project owner/admin.

This will open the batch deletion dialog requiring confirmation of the batch deletion process by clicking the Confirm button.

Attached Measurements

Keep in mind, that batches can only be deleted if none of the samples within the batch have been used in a measurement.) Otherwise, you need to delete the measurements in question before the batch can be deleted.

Download sample metadata

To download the sample metadata for all registered samples click on the Download sample metadata button. This will export all registered metadata as an .xlsx file to your local download directory.