Protocol detail

Stool DNA Extraction Protocol

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Stool specimens were handled according to the GEMS protocol (16 (link)). DNA was isolated from frozen stool specimens by using a bead beater with 3-mm diameter solid glass beads (Sigma-Aldrich, St. Louis, MO, USA) and, subsequently, with 0.1-mm zirconium beads (BioSpec Products, Inc., Bartlesville, OK, USA) to disrupt cells. The cell slurry was then centrifuged at 16,000 × g for 1 min, and the supernatant was processed by using QIAamp DNA Stool Extraction Kit (QIAGEN, Valencia, CA, USA). Extracted DNA was precipitated with ethanol and shipped to the United States.

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Lindsay B., Oundo J., Hossain M.A., Antonio M., Tamboura B., Walker A.W., Paulson J.N., Parkhill J., Omore R., Faruque A.S., Das S.K., Ikumapayi U.N., Adeyemi M., Sanogo D., Saha D., Sow S., Farag T.H., Nasrin D., Li S., Panchalingam S., Levine M.M., Kotloff K., Magder L.S., Hungerford L., Sommerfelt H., Pop M., Nataro J.P, & Stine O.C. (2015). Microbiota That Affect Risk for Shigellosis in Children in Low-Income Countries. Emerging Infectious Diseases, 21(2), 242-250.

Publication 2015

0.1-mm zirconium beads QIAamp DNA Stool Extraction Kit

Cell Ethanol Frozen Gems Stool Zirconium

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Variable analysis

independent variables

Bead beater with 3-mm diameter solid glass beads (Sigma-Aldrich, St. Louis, MO, USA)
0.1-mm zirconium beads (BioSpec Products, Inc., Bartlesville, OK, USA)

dependent variables

Not explicitly mentioned

control variables

The GEMS protocol (16 (link)) was used to handle stool specimens.
DNA was isolated from frozen stool specimens.
The cell slurry was centrifuged at 16,000 × g for 1 min.
Extracted DNA was precipitated with ethanol and shipped to the United States.

controls

No positive or negative controls were explicitly mentioned.

Annotations

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