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Quick 16s primer set v3 v4

Manufactured by Zymo Research
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The Quick-16S™ Primer Set V3-V4 is a set of primers designed for the amplification of the V3-V4 hypervariable regions of the 16S rRNA gene. The primer set is intended for use in microbiome analysis applications.

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Lab products found in correlation

Select a size dna clean concentrator, by Zymo Research (4 mentions) Tapestation, by Agilent Technologies (3 mentions) Quick 16s ngs library prep kit, by Zymo Research (2 mentions) Miseq reagent kit v3, by Illumina (1 mentions) Zymobiomics targetedsequencing service for microbiome analysis, by Zymo Research (1 mentions) Zymobiomics 96 magbead dna kit, by Zymo Research (1 mentions) Zymobiomics microbial community standard, by Zymo Research (1 mentions) Fecal dna rna shield fecal collection tubes, by Zymo Research (1 mentions) Tapestation, by Zymo Research (1 mentions) Quick 16s plus ngs library prep kit, by Zymo Research (1 mentions)

5 protocols using quick 16s primer set v3 v4

1

Microbiome Sequencing Using Quick-16S Primers

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The extracted sample DNA was sent to the ZymoBIOMICS® Targeted
Sequencing Service for Microbiome Analysis (Zymo Research, Irvine, CA) and
sequenced using the Quick-16S™ Primer set V3–V4 (Zymo Research,
Irvine, CA) via the Illumina MiSeq v3 reagent kit using a 10% PhiX spike-in.
Summary of the sequencing service: PCR products were quantified with qPCR
fluorescence readings and pooled together based on equal molarity. The pooled
library was cleaned using the Select-a-Size DNA Clean & Concentrator™
(Zymo Research, Irvine, CA), then quantified with TapeStation® Santa
Clara, CA) (Agilent Technologies, (Thermo Fisher Scientific, Waltham, WA).
Jenkins S.V., Robeson MS I.I., Griffin R.J., Quick C.M., Siegel E.R., Cannon M.J., Vang K.B, & Dings R.P. (2019). Gastrointestinal tract dysbiosis enhances distal tumor progression through suppression of leukocyte trafficking. Cancer research, 79(23), 5999-6009.
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2

Targeted Metagenomics of Fecal Samples

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At the time of processing, fecal samples were thawed, mixed, and placed (1 g) into fecal DNA/RNA shield fecal collection tubes (Zymo Research, Irvine, CA). Samples were sent to be further processed and analyzed through the ZymoBIOMICS Service: Targeted Metagenomic Sequencing (Zymo Research, Irvine, CA). The ZymoBIOMICS-96 MagBead DNA Kit (Zymo Research, Irvine, CA) was used to extract the DNA from fecal samples. The DNA samples were prepared for targeted sequencing with the Quick-16 NGS Library Prep Kit (Zymo Research, Irvine, CA). The ZymoBIOMICS Microbial Community Standard (Zymo Research, Irvine, CA) was used as a positive control for each DNA extraction and targeted library preparation. Negative controls (i.e., blank extraction control, blank library preparation control) were included to assess the level of bioburden carried by the wet-lab process. The V3–V4 region (primers 341F-806R) of the 16S rRNA gene was amplified with Quick-16S Primer Set V3–V4 (Zymo Research, Irvine, CA). The final amplicon sizes, including primers, was ~350bp and ~460bp, respectively. The final library was sequenced on Illumina MiSeq with a v3 reagent kit (600 cycles). The sequencing was performed with >10% PhiX spike-in.
Slanzon G.S., Ridenhour B.J., Moore D.A., Sischo W.M., Parrish L.M., Trombetta S.C, & McConnel C.S. (2022). Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease. PLoS ONE, 17(1), e0262317.
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3

Quick-16S Targeted Sequencing Protocol

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The DNA samples were prepared for targeted sequencing using custom targeted primer sets [Quick-16S™ Primer Set V3-V4 (Zymo Research, Irvine, CA)] with the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA). The sequencing library was performed in real-time PCR to control cycles and therefore prevent PCR chimera formation. The final PCR products were pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™ (Zymo Research, Irvine, CA), then quantified with TapeStation® and Qubit®.
Can-Herrera L.A., Gutierrez-Canul C.D., Dzul-Cervantes M.A.A., Pacheco-Salazar O.F., Chi-Cortez J.D, & Carbonell L.S. (2021). Identification by molecular techniques of halophilic bacteria producing important enzymes from pristine area in Campeche, Mexico. Brazilian journal of biology = Revista brasleira de biologia, 83.
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4

16S rRNA Gene Targeted Sequencing

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The DNA samples were prepared for targeted sequencing with the Quick-16S™ Plus NGS Library Prep Kit (Zymo Research, Irvine, CA). These primers were custom designed by Zymo Research to provide the best coverage of the 16S gene while maintaining high sensitivity. Quick-16S™ Primer Set V3-V4 (Zymo Research, Irvine, CA) was used to amplify the targeted region of the microbial 16Sgene. The sequencing library was prepared using an innovative library preparation process in which PCR reactions were performed in real-time PCR machines to control cycles and therefore, limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™(Zymo Research, Irvine, CA), then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA).
Hunter C., Dia K., Boykins J., Perry K., Banerjee N., Cuffee J., Armstrong E., Morgan G., Banerjee H.N., Banerjee A, & Bhattacharya S. (2024). An investigation for phylogenetic characterization of human Pancreatic cancer microbiome by 16SrDNA Sequencing and Bioinformatics techniques. Research Square.
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5

Targeted 16S rRNA Gene Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols
The DNA samples were prepared for targeted sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA, USA). These primers were custom-designed by Zymo Research to provide the best coverage of the 16S gene while maintaining high sensitivity. The primer sets used in this project were Quick-16S™ Primer Set V3-V4 (Zymo Research, Irvine, CA, USA).
The sequencing library was prepared using an innovative library preparation process in which polymerase chain reactions (PCR) were performed in real-time PCR machines to control cycles and therefore limit PCR chimera formation. The final PCR products were quantified with qPCR fluorescence readings and pooled together based on equal molarity. The final pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™ (Zymo Research, Irvine, CA, USA), then quantified with TapeStation® (Agilent Technologies, Santa Clara, CA, USA) and Qubit® (Thermo Fisher Scientific, Waltham, WA, USA).
Hursitoglu M., Kural A., Kuras S., Akdeniz E., Sezer S., Caypinar S.S., Kazezoglu C., Yaprak B., Karandere F, & Guven H.Z. (2021). MATERNAL GUT MICROBIOTA IN PREGNANCIES RESULTING IN DOWN SYNDROME NEWBORNS – A PILOT STUDY. Acta Clinica Croatica, 60(4), 722-730.
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