Table 1.

Key methodological features of FB5P-seq, Smart-seq2, and 10x Genomics 5′-end integrative scRNA-seq methods.

	FB5P-seq	Smart-seq2	10× Genomics 5′-end
Cell capture	FACS-based	FACS-based	Droplet-based
Analysis of phenotypic markers	From FACS staining and index sorting May include fluorescent reporters or indicators	From FACS staining and index sorting May include fluorescent reporters or indicators	From DNA-barcoded antibody stainings (e.g., CITE-seq) Limited to surface markers
Cell throughput	One cell/well in 96-well plate format Multiplex up to 16 plates per sample (our experience)	One cell/well in 96-well plate format Multiple plates may be multiplexed	Up to 10,000 cells per run Multiple runs may be done in parallel
cDNA barcoding	RT with template switching 5′-end barcoding with UMI	RT with template switching No cDNA barcoding, no UMI	RT with template switching 5′-end barcoding with UMI
Sequencing library	One library per 96-well plate	One library per cell	One library per run for gene expression One library per run for BCR One library per run for TCR One library per run for surface markers
Recommended sequencing depth	5 × 105 reads/cell Paired-end, single-index	1 × 106 reads/cell Single-end or paired-end, dual-index	5 × 104 reads/cell for gene expression 5 × 103 reads/cell for BCR/TCR 5 × 103 reads/cell for surface markers Paired-end, single-index
Sensitivity (for PBMC, B/T cells)	1,000–2,000 genes/cell	2,000–3,000 genes/cell	1,000–2,000 genes/cell