Question: Can I sequence V(D)J-enriched and 5' Gene Expression libraries on the same lane?
Answer: Yes. V(D)J-enriched libraries and 5’ Gene Expression libraries can be pooled for sequencing, but note the depth requirements and sequencing configurations are different. We recommend 5,000 reads/cell for V(D)J-enriched libraries and 50,000 reads/cell for 5’ Gene Expression libraries, and therefore recommend adjusting the pooling ratio accordingly. (For example, if the two library types have the same number of cells targeted and the same library concentration, 10-fold more 5' Gene Expression Library should be mixed with the V(D)J-enriched Library to obtain 10x more reads per cell.)
If pooling library types, 5' Gene Expression libraries can be sequenced using V(D)J-enriched library parameters (Read 1: 150 cycles, i7: 8 cycles, Read 2: 150 cycles), however it should be noted that the cost of sequencing using enriched library parameters is higher because more cycles are needed. 5' Gene Expression sequencing parameters should not be used on pooled samples.