Question: What are the protocol differences between Single Cell 3' v3.1 Single Index and 3' v3.1 Dual Index?
Answer: The 3' v3.1 Single Index and 3' v3.1 Dual Index assays have different library preparation protocols, to incorporate single or dual indexes. The upstream steps of the assay (GEM generation, reverse transcription, cDNA amplification) are identical between the Single Index and Dual Index assays.
The different library preparation protocols make use of different primers, as shown for the three library types below.
1) For Gene Expression libraries, the SI Primer and Single Index Plate T Set A are used to prepare Single Index libraries, whereas the Dual Index Plate TT Set A is used to prepare Dual Index libraries.
Note that the "SI Primer" should not be used when preparing dual index libraries. Please also see: Can I use the SI Primer together with Dual Index Plate TT when preparing Single Cell 3' Gene Expression libraries?
2) For Cell Surface Protein libraries, the Feature SI Primers 2 and Single Index Plate T Set A are used to prepare Single Index libraries, whereas the Dual Index Plate NT Set A is used to prepare Dual Index libraries.
3) For CRISPR Screening libraries, the Feature SI Primers 1, Feature SI Primers 2 and Single Index Plate T Set A are used to prepare Single Index libraries, whereas the Feature SI Primers 3 and Dual Index Plate NT Set A are used to prepare Dual Index libraries.
Product: Single Cell Gene Expression