Is the Seeker kit compatible with Element Biosciences’ AVITI sequencer?

Yes, Seeker libraries are compatible with Element Biosciences’ AVITI sequencer after conversion of the generated Illumina library to an AVITI library using the following protocol: Element Adept Library Compatibility Kit v1.1 https://www.elementbiosciences.com/products/adept" target="_blank https://www.elementbiosciences.com/products/adept [...]

What is the recommended number of reads when your sample tissue does not cover the entire tile area?

Recommended reads and saturation metrics for partial tile coverage: For a 3x3 tile that is fully covered by the tissue section, we suggest 30 million reads for shallow sequencing or 2 x 10 8 reads for deep sequencing, based on data generated with mouse hippocampus. If your tissue section does not cover the entire tile area, you can lower the number of reads based on the estimated percent of tile [...]

How much PhiX should I spike in to my library before sequencing?

We recommend using the same recommendations as those for the NovaSeq 6000, as outlined in the user guide.  Phi-X spike-in recommendations: NextSeq 1000/2000: 5% PhiX spike-in NextSeq 500/550: 5% PhiX spike-in NovaSeq 6000/X Plus: 5% PhiX spike-in when pooling with non-Seeker libraries 10% PhiX spike-in when sequencing only Seeker libraries [...]

How deep should I sequence Seeker libraries?

Although we recommend 2 x 10 8 –6 x 10 8 paired-end reads for the 3 mm x 3 mm tile and 2 x 10 8 –3 x 10 8 billion paired-end reads for the 10 mm x 10 mm tile, deeper sequencing may be required for more transcriptionally active tissue types. In the HTML Seeker Primary Analysis Pipeline, the metric "median reads/UMI" indicates the approximate sequencing saturation. We recommend a value of 8–10 to [...]

For the Dual Indexing Primer kit, what orientation are the sequences listed in the User Guide table?

For the following table: [...]