Table 1.

Sequencing yield and quality of V2 inDrop with/without standard illumina libraries

Sequencing Run	Sequencer	Sequencing Kit	Targeted inDrop read depth	Observed inDrop read depth	Mean transcript Quality Score	Mean Barcodes and UMI Quality
V2 structure mouse 1	NextSeq	Mid-throughput	130,000,000	148,238,920	30.72	30.55
V2 structure mouse 1 + 10% illumina PhiX	MiSeqa	Nano	900,000	745,903	34.94	32.24
V2 structure mouse 2 and 3 + 15% illumina PhiX	NextSeq	Mid-throughput	110,500,000b	122,520,660	33.09	33.08

^aIt is thought that the inDrop reads (745,903) for the MiSeq test was lower than the expected 1 million reads due to the fact that the loading concentration of inDrop libraries has been optimized on the NextSeq, but not on the MiSeq. On the NextSeq we have found that loading the inDrop libraries at 1.5x the listed optimal loading concentration improves clustering efficiency on the flow cell. The loading concentration of inDrop libraries on the MiSeq for this sequencing run was just the standard loading concentration

^bThe targeted read depth is slightly decreased here compared to that of the V2 Structure mouse 1 because 15% of the read depth is expected to be taken up by PhiX