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Table 1 Sequencing yield and quality of V2 inDrop with/without standard illumina libraries

From: Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms

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
  1. 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
  2. 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