The Sample Loading Table module of TrailmakerTM supports the generation and export of sample loading tables for the following Parse Biosciences EvercodeTM kits, compatible with v2, v3 and v4 chemistry, and both manual and automated workflows:
- Whole Transcriptome (WT) Mini, WT, WT Mega
- TCR Mini, TCR, TCR Mega
- BCR Mini, BCR, BCR Mega
Sample loading tables for WT Mega 384, WT Penta, WT Penta 384 and WT FFPE kits are not currently supported on Trailmaker and instead customers can download the Excel version on our support suite.
On the first visit to the Sample Loading Table module, click 'Create Sample Loading Table' to get started.
Input a name for the new sample loading table and click 'Create'.
The new sample loading table will appear in your list of tables and will be selected by default. The Sample Loading Table Details tile on the right side of the page shows section 1 'Samples & Cells' of the selected sample loading table.
Section 1 'Samples & Cells'
Input the experiment information including kit type, kit chemistry, number of samples and target number of barcoded cells. When the kit type is input, further fields appear automatically. Note that the default target number of barcoded cells is preset as the recommended maximum cell load for each kit size.
When you are ready to continue, click ‘Next Step’.
Section 2 'Sample Information'
Input the sample names together with the percent of library allocation and stock concentration (in cells/uL) for each sample. If you are running samples of unequal proportions, input samples into the sample loading table from highest to lowest percentage allocation.
When you are ready to continue, click ‘Next Step’. Two buttons will appear:
- The 'Save to Trailmaker' button allows you to save the sample loading table within Trailmaker. Saved sample loading tables can be used as inputs to the FASTQ file processing pipeline in the Pipeline module of Trailmaker.
- The 'Download Spec List File' button allows you to download the Sample Specification List file. This file specifies which samples are in which wells and can serve as an input for running the FASTQ processing pipeline outside of Trailmaker.
Section 3 ‘Table Data, Volumes, and Plate Configurations’
The Sample Loading Table and Plate Configuration can be viewed and downloaded.
- The Sample Loading Table provides the required volumes of sample stock and dilution buffer to prepare the sample working dilutions for loading into the Round 1 barcoding plate(s) for each selected kit. Use the indicated volumes to prepare the appropriate working dilution for each sample prior to loading.
- The Plate Configuration illustrates which samples should be added to which wells in the round 1 plate. At the top is a 96-well plate layout, with the color-coordinated sample reference table shown underneath. The sample names automatically populate the sample reference table. The number of wells used per sample is automatically populated, with each sample assigned a color. The colored plate configuration has been arranged to correspond to the appropriate samples and number of wells.
These files are easy to download and print in order to take to the bench for reference when loading the round 1 barcoding plate.
Section 4 'Integra Tables & Downloads'
If required, the Integra tables can be generated and downloaded in Section 4 by clicking ‘Generate Tables and Files’.
The Integra Worklist File can be downloaded using the button. This file serves as an input for running an Integra workflow.
The Integra Loading Table can be viewed by clicking the relevant arrow to maximize the table.
The Diluent Volumes can be viewed by clicking the relevant arrow to maximize the diluent volumes table.
Unsaved changes
If you have unsaved changes in your sample loading table, the following warning message will appear if you navigate away:
To save your sample loading table, click the 'Save to Trailmaker' button after section 2:
Using a sample loading table to run the pipeline
Saved sample loading tables from this module can be directly imported to the Trailmaker Pipeline module for FASTQ file processing. Alternatively, sample loading tables can be downloaded from this module and used as input for running the Parse pipeline locally.