Table 1.

Quality control metrics: quality control data represent six samples across two separate experiments. The average and SD for all metrics is represented.

Sequencing metrics
Sample	No. of reads	Valid barcodes (%)	Valid UMIs (%)	Sequencing saturation (%)	Q30 bases in barcode (%)	Q30 bases in RNA read (%)	Q30 bases in UMI (%)
C1	229,291,982	96.7	99.9	72.7	96.4	93.7	96.2
C2	268,498,276	96.2	100	36.9	95.2	92.1	94.9
m1	243,061,000	96.6	99.9	79	96.3	93.1	96.2
M1	110,311,933	95.2	99.9	91.8	96.4	94.5	96.3
M2	252,256,865	97.3	99.9	88.6	96.5	94	96.4
M3	226,248,973	96.2	100	37.7	95	91.9	94.7
MEAN	221,611,504.8	96.4	99.9	67.8	96.0	93.2	95.8
STDV	56,684,528.4	0.7	0.1	24.6	0.7	1.0	0.8
Read mapping metrics
Sample	Mapped to genome (%)	Mapped confidently to genome (%)	Mapped confidently to intergenic regions (%)	Mapped confidently to intronic regions (%)	Mapped confidently to exonic regions (%)	Mapped confidently to transcriptome (%)	Mapped antisense to gene (%)
C1	96.8	92.9	6.2	54.8	31.9	69.4	15.9
C2	92.5	87.7	7	61.3	19.4	44.2	35.4
m1	96.7	93.3	6.3	56.3	30.6	67.8	17.7
M1	92.9	65.1	6.6	40.1	18.3	52.8	4.1
M2	96.2	91.4	7.5	54.8	29.1	72.6	9.4
M3	91.4	86	7.2	58.9	19.9	44	33.7
MEAN	94.4	86.1	6.8	54.4	24.9	58.5	19.4
STDV	2.4	10.7	0.5	7.4	6.3	13.0	12.7
Cell metrics
Sample	Recovered nuclei	Fraction reads in nuclei (%)	Mean reads per nucleus	Median genes per nucleus	Total genes detected	Median UMI counts per nucleus
C1	9,697	89.4	23,345	1,409	26,472	3,232
C2	13,030	90.8	20,565	1,981	28,120	4,729
m1	8,531	91.1	28,279	1,344	26,198	3,008
M1	1,161	60.6	87,914	771	19,440	1,221
M2	3,944	79.1	61,406	1,533	26,062	2,730
M3	6,997	86.9	32,183	2,469	28,497	6,654
MEAN	7,226.7	83.0	42,282.0	1,584.5	25,798.2	3,595.7
STDV	4,221.5	11.8	26,744.4	581.8	3,279.8	1,871.0