Extended Data Fig. 2: Spike-in validation. | Nature Microbiology

Extended Data Fig. 2: Spike-in validation.

From: Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows

Extended Data Fig. 2

a, RT-PCR for an SDSI in water and a SARS-CoV-2 positive clinical sample background. Mastermix and SDSI specific primers were added to all samples. SARS-CoV-2 positive clinical sample is cDNA generated from a nasopharyngeal (NP) swab. b, The distribution of GC content and length for ARTIC v3 primers. c, The distribution of GC content of SDSI amplicons (n = 96). d, 100fmol DNA spike-in amplified under standard ARTIC PCR conditions for 40 cycles run on 2.2% agarose gel image with 188 bp amplified spike-in (SDSI 1-48) (n = 2, representative image shown). e, % SDSI reads over total reads for SDSI (2-48) over a range of SDSI GC% (33%-65.4%) showed no significant read depth bias. Data are presented as mean values + /- 95% CI. Linear regression: p-value=0.8160, R2 = 2.038e-005 (Broad, n = 2,903 biologically independent samples).

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