sequencing depth in ScRNASeq

Question

[kanwarjag]

In 10X single cell RNAseq how can be achieve a good sequencing depth to detect lowly expressed genes. Soemthing similar has been shown in this paper https://www.nature.com/articles/nbt.2967 to get a good sequencing depth in a microfluidics system. Is better sequencing depth is possible in micro fluid system and not in 10X genomics? An thoughts. I looked at web page of 10X genomics but could not find answers.

Thanks

[rob.costa1234]

Though it is an old thread but question seems to be relvant I ran 10x samples in MiSeq and estimated cells around 2000. However, Miseq suggest around 50 cells per sample. QC of FASTA files is good. If the sequencing is done on nova seq. or another sequencer -next seq will it capture more cells? Does that indicate cell death

Answer 1

[Devon Ryan]

10x is a microfluidics system. If you want more depth then either sequence more or use fewer cells.