Question: Why has the loading concentration on the NovaSeq 6000 Illumina sequencing platform been updated for Next GEM library types?
Answer: To improve sequencer output, we have adjusted our loading concentration so users can maximize their sequencing runs for the libraries generated by the following 10x Genomics assays on the NovaSeq 6000 Illumina sequencing platform:
- Chromium Next GEM Single Cell 3’ Gene Expression (v3.1 Dual Index, HT v3.1)
- Chromium Next GEM Single Cell 5’ Gene Expression (v2, HT v2)
- Chromium Next GEM Single Cell ATAC v2
- Chromium Next GEM Single Cell Multiome ATAC + Gene Expression
To improve the robustness of sequencing runs, we are updating our loading recommendations for the NovaSeq 6000 as follows:
- NovaSeq 6000 Standard Workflow: 150 pM (previous guidance was 300 pM)
- NovaSeq 6000 XP Workflow: 150 pM (unchanged from previous guidance of 150 pM)
For the NovaSeq 6000 Standard Workflow, we have observed that using a loading concentration of 150 pM instead of 300 pM for the libraries generated by the above assays may slightly improve the percentage of clusters passing filter, Q30 scores, demultiplexing efficiency, and total data output (number of usable reads).
For general guidance on optimizing loading concentrations for NovaSeq 6000, refer to Illumina’s tutorial for plotting % Occupied by % Pass Filter.
We will be revising the User Guides for each of the Next GEM assays above to include this updated guidance for the NovaSeq 6000 sequencing platform. For other Illumina sequencers, the recommended loading concentrations remain unchanged.
Products: Single Cell Gene Expression, Single Cell Immune Profiling, Single Cell Multiome ATAC + Gene Expression, Single Cell ATAC