Overcoming Common Challenges in Single Cell RNA-seq Experiments with PIPseq: UCSF Case Study

Species-Mixture Experiment

(HEK 293/NIH 3T3)

1:1 Mixture of Human HEK293 and Mouse NIH3T3 cells purchased by Fluent BioSciences from ATCC were used in a standard species-mixture experiment to demonstrate the capabilities of PIPseq.

5400 cells were input into a T2 PIPseq reaction, resulting in 2,706 captured cells. Libraries were generated using PIPseq v3.0 chemistry and sequenced on an Illumina NextSeq 2000 to a depth of 108,000,000 reads (~40k reads per cell).

Samples were sequenced using paired-end dual indexing with the following settings:

  • Read 1: 51 cycles
  • i5 index 8 cycles
  • i7 index 8 cycles
  • Read 2: 70 cycles

Processed with PIPseeker v1.1.3 using –force-cells 2706