Table S1.

Optimizing recovery of gDNA and HIV RNA for CARD-SGS

Recovery of gDNA measured by CCR5 copies		Digestion of gDNA from ACH-2 cells by DNase I		Digestion of HIV DNA from donor PBMCs at an end point for CARD-SGS by DNase I
No. of PBMCs or ACH-2 cells extracted	Recovery of gDNA, %	No. of HIV proviruses before treatment with DNase I	No. of HIV proviruses detected in no RT control after DNase I digestion*	No. of HIV proviruses in patient sample before treatment with DNase I†	No. of HIV proviruses detected in no RT controls after DNase I digestion†	No. of HIV RNA copies after digestion with DNase I*
2,000,000	36‡	9,382,973	145	280	0	5
1,000,000	52‡	2,734,645	9	235	0	5
600,000	145§	1,218,179	9	140	0	13
200,000	59	233,347	0	42	0	27
66,667	70	133,357	0
22,222	60	36,848	0
7,407	48	5,493	0
2,469	62

^*HIV copies were measured by qPCR (11).

^†HIV copies were measured by end-point dilution PCR of the P6-PR-RT target used for the other studies presented here. Gray shading indicates the highest level of recovery of gDNA was from 600,000 cells.

^‡Average of triplicates measured by qPCR for CCR5 copy number. PBMCs were stored at −80 °C for 3–12 mo before extraction.

^§Twofold deviation of qPCR measurements suggests that recovery was likely 100%.