Control type | Control subtype | Control name | Composition | Source | DNA extraction performed in our laboratory | DNA extraction kit | Extraction replicates | Sequencing replicates | Total included for equencing |
---|---|---|---|---|---|---|---|---|---|
Extraction controls | Bacterial mock communities | Zymobiomics-Primestore-high | 900 μl of Zymobiomics-Cells suspended in 3600 μl Primestore | Zymo Research Corp., Irvine, CA, United States & Longhorn Vaccines & Diagnostics, Bethesda, MD, USA | ✓ | Kit-QS Kit-ZB | 3 per DNA extraction kit | – | 6 |
Zymobiomics-STGG-high | 900 μl of Zymobiomics-Cells suspended in 3600 μl STGG | Zymo Research Corp., Irvine, CA, United States & National Health Laboratory Services, Cape Town, South Africa | ✓ | Kit-QS Kit-ZB | 3 per DNA extraction kit | – | 6 | ||
Zymobiomics-Primestore-low | 1-in-104 fold dilution of Zymobiomics-Primestore-high | Zymo Research Corp., Irvine, CA, United States & Longhorn Vaccines & Diagnostics, Bethesda, MD, USA | ✓ | Kit-QS Kit-ZB | 3 per DNA extraction kit | – | 6 | ||
Zymobiomics-STGG-low | 1-in-104 fold dilution of Zymobiomics-STGG-high | Zymo Research Corp., Irvine, CA, United States & National Health Laboratory Services, Cape Town, South Africa | ✓ | Kit-QS Kit-ZB | 3 per DNA extraction kit | – | 6 | ||
NTCs | Primestore | Storage buffer Primestore | Longhorn Vaccines & Diagnostics, Bethesda, MD, USA | ✓ | Kit-QS Kit-ZB | 3 per DNA extraction kit | – | 6 | |
STGG | Storage buffer STGG | National Health Laboratory Services, Cape Town, South Africa | ✓ | Kit-QS Kit-ZB | 3 per DNA extraction kit | – | 6 | ||
Sequencing controls | Bacterial mock community DNA | BEI-DNA | 1-in-10 fold dilution of HM-783D in Milli-Q® ultrapure water | BEI Resources, NIAID, NIH as part of the Human Microbiome Project, Manassas, VA, USA & MilliporeSigma, Burlington, MA, USA | x | Not specified | – | – | 3 |
Zymobiomics-DNA | 1-in-10 fold dilution of ZymoBIOMICS™ Microbial Community DNA Standard in Milli-Q® ultrapure water | Zymo Research Corp., Irvine, CA, United States & MilliporeSigma, Burlington, MA, USA | x | Not specified | – | – | 8 | ||
Technical repeats | Within-run repeats | NP and IS specimens stored in Primestore | Collected from infants enrolled in the DCHS [26] | ✓ | Kit-QS | – | 2 per specimen | 86 | |
Between-run repeats | NP and IS specimens stored in Primestore | Collected from infants enrolled in the DCHS [26] | ✓ | Kit-QS | – | 2, 3 or 4 per specimen | 123 | ||
NTCs | Primestore | Storage buffer Primestore | Longhorn Vaccines & Diagnostics, Bethesda, MD, USA | ✓ | Kit-QS | – | – | 35 |