Can I run the Trekker bioinformatics pipeline on my Mac or Windows computer?

No. The Trekker pipeline only runs on Linux Systems. For system requirements, please visit our https://knowledgebase.curiobioscience.com/bioinformatics/trekker-local-installation-latest/ local installation guide #_msocom_1 [...]

How is Trekker data analyzed?

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. The pipeline can be downloaded from our knoThe pipeline can be downloaded from our knowledge base #_msocom_1 [...]

Will I see a batch effect if I split nuclei from a single tissue slice into multiple lanes for sequencing?

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 redoing normalization on the merged dataset, either through counts per million (CPM) or SCT (from Seurat) methods, #_msocom_1 [AR1] #_msocom_2 [PH2] before performing in-depth [...]

Can I align my Trekker data to an H&E image on an adjacent section?

Yes. We have used https://www.nature.com/articles/s41467-023-43915-7 STalign to successfully align H&E staining and Trekker data. For further information, please check out https://jef.works/STalign/notebooks/xenium-heimage-alignment.html STalign's [...]

What is the recommended way to ‘bank’ samples for batch processing?

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 [...]