title: 16S rRNA V3-4 gene amplicon sequencing of kidney stone sample (341F/785R) [JMF-2102-05-0112B]
design: Amplicon sequencing of kidney stone sample. Catheterized urine and kidney stones were collected intraoperatively from 100 patients undergoing endoscopic nephrolithotomy. Voided urine of 20 volunteers served as control. Samples were processed within 30 min after removal: Stones were snap frozen in liquid nitrogen. Urine was centrifuged at 3000 rcf for to 10 min at 4C; supernatant was discarded and the pellet snap frozen. All samples were stored at -80C until further processing. Stones were grounded by beat beating, prior to DNA extraction using the 47016 DNA-EASY PowerSoil Kit (Quiagen), according to the manufacturer's instructions. For DNA extraction from pelleted urine samples the 51704 QIAAMP DNA Microbiome Kit (Quiagen) was used, according to the manufacturer's instructions. Sequencing was performed as described in https://doi.org/10.3389/fmicb.2021.669776. {primers: CCTACGGGNGGCWGCAG + GACTACHVGGGTATCTAATCC, nucleic acid: DNA, flow cell identifier: JV7LD, barcoding: UDB-H12, plate-position: 2 H3, barcodes: CTCACGCAATGC + CTCACTGCTTCT}.