Trekker FAQs

The Trekker reagent kit converts single-cell data into a spatial map by spatially tagging nuclei from a tissue section before running them on a typical single-cell sequencing platform. See product page for more details.

A simple UV lamp fixture (Cat. # K011), purchased as a starter kit (see product page). Please note that different UV lamp fixtures are available based on regional compatibility.

We have optimized the assay on the UV lamp in the starter kit bundle (Cat. # K011). We cannot guarantee performance based on different UV lamps and do not recommend deviating from the lamp provided.

~1 hour protocol added before single-cell sequencing library preparation.

10 mm x 10 mm

25 microns (µm)

Currently, the Trekker kit is compatible with fresh frozen tissues.

The Trekker kit has successfully been applied to samples from mouse brain, kidney, liver, embryo, colon, lung, testis, and spleen, as well as human brain, breast cancer, and melanoma. Please contact your local Takara Bio representative for more information on compatible tissue types. The Trekker protocol should be compatible with most tissues, but some may require optimization of nuclei dissociation to maximize recovery. 

The Trekker kit is currently compatible with fresh frozen tissues. Please contact your local Takara Bio representative for more information regarding compatibility with FFPE tissues.

Optimization of nuclei dissociation can help ensure the best results for your experiment. We recommend optimizing your nuclei dissociation protocol with 25 micron-thick frozen tissue sections before starting a Trekker experiment. We provide training tiles as a purchasable product (Cat. # SK020) for practice with off-tile tissue dissociation and Trekker tile handling. We also highly recommend consulting with the Takara Bio technical support team for guidance specific to your tissue of interest.

Our protocol supports freezing the tile with the melted tissue at –80°C for up to 4 days (before UV cleavage).

To process two samples in parallel, section and mount the tissue onto the first tile and start UV cleavage. If tiles with tissue sections were previously stored at –80°C, briefly melt the tile with a finger and proceed to the UV cleavage step.

During the 7.5 min incubation, prepare the second tile and start UV cleavage. Perform tissue dissociation of the first tile followed by the second tile, making sure to add Buffer B within 10 min of adding Buffer A.

When both samples are in Buffer B, centrifuge and complete the rest of the protocol in parallel. If desired, you may start another set of two samples while the first set undergoes the first centrifugation step.

We have observed minimal lane-to-lane batch effect, so integration across different lanes is not required. Nevertheless, consistent normalization should be performed on the merged dataset. We recommend repeating normalization on the merged dataset, either through counts per million (CPM) or SCT (from Seurat) methods, before performing in-depth analysis.

Currently, the Trekker kit is compatible with 10x Chromium and BD Rhapsody Single-Cell Analysis System. Additional Trekker technology users have successfully demonstrated compatibility with other single-cell workflows, Please contact your local Takara Bio representative for more information.

Currently, the Trekker kit is compatible with 10x Chromium Next GEM Single Cell 3′ v3.1, 10x Chromium GEM-X Single Cell 3′ v4, and BD Rhapsody Whole Transcriptome Analysis kits. Additional Trekker technology users have successfully demonstrated compatibility with other single-cell workflows, including the BD Rhapsody Single-Cell ATAC-Seq and mRNA Whole Transcriptome Analysis Kit as well as the BD Rhapsody Single-Cell TCR/BCR Next and mRNA Whole Transcriptome Analysis Kit. Please contact your local Takara Bio representative for more information regarding compatibility with these single-cell platforms.

We have successfully sequenced the Trekker library on the Illumina NextSeq® 1000/2000, Illumina NovaSeq™ X, and the Element AVITI. The gene expression library can be sequenced on any sequencer supported by the single-cell platform of choice.

Sequencing depth for the Trekker library, like most gene expression libraries, should be adjusted according to the user guide of the relevant single-cell platform. For 10x Chromium, sequence the Trekker library at a depth of 5,000 read pairs per nucleus captured.

For BD Rhapsody, sequence the Trekker library at a depth of 1,000 read pairs per nucleus captured.

We provide a bioinformatics pipeline that combines the single-nuclei sequencing output with the spatial barcode information from the Trekker kit to position the nuclei recovered from single-nuclei sequencing onto a spatial map.

Please contact our technical support team for guidance on how to access our pipeline.

You can locally install and execute the pipeline on a Linux server or with HPC (high-performance computing). The pipeline can also be executed in a push-button fashion on our cloud platform. 

Please contact our technical support team for more details on both methods.

No. The Trekker pipeline only runs on Linux Systems. For system requirements, please contact our technical support team.

Yes. We have used STalign to successfully align H&E (hematoxylin and eosin) staining and Trekker data. For further information, please check out the tutorial from STalign.