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Quant it hs dsdna reagent kits

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The Quant-iT HS dsDNA reagent kits are laboratory equipment used for the quantification of double-stranded DNA (dsDNA) samples. These kits employ a sensitive fluorescent dye that binds to dsDNA, enabling accurate measurement of DNA concentrations in a wide range of sample types.

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Lab products found in correlation

Axyprep magpcr clean up beads, by Corning (4 mentions) Miseq instrument, by Illumina (3 mentions) Fragment analyzer, by Agilent Technologies (2 mentions) Eb buffer, by Qiagen (2 mentions) Phusion high fidelity dna polymerase, by Thermo Fisher Scientific (2 mentions) Powerfecal kit, by Qiagen (1 mentions)

5 protocols using quant it hs dsdna reagent kits

1

16S rRNA amplicon sequencing of gut microbiome

Cited 4 times
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Feces from RA, RA+PA, IH, and IH+PA mice, as well fecal samples from FMT treated mice were processed using PowerFecal kits (Qiagen) according to the manufacturer's instructions [26 (link), 51 (link), 52 (link)]. Briefly, bacterial 16S rRNA amplicons were constructed via amplification of the V4 region of the 16S rRNA gene with universal primers (U515F/806R) as previously developed against the V4 region, flanked by Illumina standard adapter sequences [53 (link), 54 (link)]. The final amplicon pool was evaluated using the Advanced Analytical Fragment Analyzer automated electrophoresis system, quantified using quant-iT HS dsDNA reagent kits, and further diluted according to Illumina's standard protocol for sequencing on the MiSeq instrument.
Paired DNA sequences were merged using FLASH software [55] (link). Cutadapt (https://github.com/marcelm/cutadapt) was used to remove the primers at both ends of the contig and cull contigs that did not contain both primers. Taxonomy was assigned to selected OTUs using BLAST against the SILVA database v128 of 16S rRNA sequences and taxonomy [56 (link), 57 (link)].
Khalyfa A., Ericsson A., Qiao Z., Almendros I., Farré R, & Gozal D. (2021). Circulating exosomes and gut microbiome induced insulin resistance in mice exposed to intermittent hypoxia: Effects of physical activity. EBioMedicine, 64, 103208.
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2

16S rRNA Amplicon Sequencing Protocol

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Extracted fecal DNA was used to generate libraries at the MU DNA Core Facility. Bacterial 16S rRNA amplicons were constructed via amplification of the V4 region of the 16S rRNA gene using dual-indexed universal primers (U515F/806R) previously developed against the V4 region, flanked by Illumina standard adapter sequences(Loy et al., 2007 (link); Caporaso et al., 2011 (link)). Oligonucleotide sequences are available at proBase. PCR was performed in 50 μL reactions containing 100 ng metagenomic DNA, primers (0.2 μM each), dNTPs (200 μM each), and Phusion high-fidelity DNA polymerase (1U). Amplification parameters are 98°C(3 min) + [98°C(15 sec) + 50°C(30 sec) + 72°C(30 sec)] × 25 cycles + 72°C(7 min). Amplicon pools (5 μL/reaction) were combined, mixed, and purified by addition of Axygen Axyprep MagPCR clean-up beads to an equal volume of 50 μL of amplicons and incubated for 15 min at room temperature. Products were then washed multiple times with 80% ethanol and the dried pellet resuspended in 32.5 μL EB buffer, incubated for two minutes at room temperature, and then placed on the magnetic stand for five minutes. The final amplicon pool was evaluated using an Advanced Analytical Fragment Analyzer automated electrophoresis system, quantified using quant-iT HS dsDNA reagent kits, and diluted according to Illumina’s standard protocol for sequencing on the MiSeq instrument.
Russell A., Copio J.N., Shi Y., Kang S., Franklin C.L, & Ericsson A.C. (2022). Reduced housing density improves statistical power of murine gut microbiota studies. Cell reports, 39(6), 110783.
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3

Amplicon Sequencing of Bacterial 16S rRNA

Cited 1 time
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The amplicon library preparation and sequencing occurred at the University of Missouri Genomics Technology Core facility. Bacterial 16S rRNA amplicons were constructed via amplification of the V4 region of the 16S rRNA gene with universal primers (U515F/806R) [25 (link),26 (link),27 (link)] flanked by Illumina standard adapter sequences. Dual-indexed forward and reverse primers were used in all reactions. A PCR was performed in 50 µL reactions containing 100 ng metagenomic DNA, primers (0.2 µM each), dNTPs (200 µM each), and Phusion high-fidelity DNA polymerase (1U, Thermo Fisher, Waltham, MA, USA). The amplification parameters were 98 °C(3 min) + [98 °C(15 s) + 50 °C(30 s) + 72 °C(30 s)] × 25 cycles + 72 °C(7 min). The amplicon pools were combined, mixed, and purified using Axygen Axyprep MagPCR clean-up beads for 15 min at room temperature. The products were washed multiple times with 80% ethanol and the dried pellet was resuspended in 32.5 µL of the EB buffer (Qiagen, Venlo, The Netherlands), incubated for two minutes at room temperature, and then placed on a magnetic stand for five minutes. The amplicon pool was evaluated using an Advanced Analytical Fragment Analyzer automated electrophoresis system, quantified using quant-iT HS dsDNA reagent kits, and diluted according to the Illumina standard protocol for sequencing as 2 × 250 bp paired-end reads on the MiSeq instrument.
Cheatham C.N., Gustafson K.L., McAdams Z.L., Turner G.M., Dorfmeyer R.A, & Ericsson A.C. (2023). Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice. Microorganisms, 11(2), 484.
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4

16S rRNA Amplicon Sequencing Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
Extracted fecal DNA was used to generate libraries at the MU DNA Core Facility. Bacterial 16S rRNA amplicons were constructed via amplification of the V4 region of the 16S rRNA gene using dual-indexed universal primers (U515F/806R) previously developed against the V4 region, flanked by Illumina standard adapter sequences(Loy et al., 2007 (link); Caporaso et al., 2011 (link)). Oligonucleotide sequences are available at proBase. PCR was performed in 50 μL reactions containing 100 ng metagenomic DNA, primers (0.2 μM each), dNTPs (200 μM each), and Phusion high-fidelity DNA polymerase (1U). Amplification parameters are 98°C(3 min) + [98°C(15 sec) + 50°C(30 sec) + 72°C(30 sec)] × 25 cycles + 72°C(7 min). Amplicon pools (5 μL/reaction) were combined, mixed, and purified by addition of Axygen Axyprep MagPCR clean-up beads to an equal volume of 50 μL of amplicons and incubated for 15 min at room temperature. Products were then washed multiple times with 80% ethanol and the dried pellet resuspended in 32.5 μL EB buffer, incubated for two minutes at room temperature, and then placed on the magnetic stand for five minutes. The final amplicon pool was evaluated using an Advanced Analytical Fragment Analyzer automated electrophoresis system, quantified using quant-iT HS dsDNA reagent kits, and diluted according to Illumina’s standard protocol for sequencing on the MiSeq instrument.
Russell A., Copio J.N., Shi Y., Kang S., Franklin C.L, & Ericsson A.C. (2022). Reduced housing density improves statistical power of murine gut microbiota studies. Cell reports, 39(6), 110783.
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5

Amplicon Sequencing of 16S rRNA V4 Region

Cited 1 time
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Library preparation and sequencing were performed at the University of Missouri Genomics Technology Core. Bacterial 16S rRNA amplicons were constructed via amplification of the V4 region of the 16S rRNA gene with universal primers (U515F/806R)27 (link) previously developed against the V4 region, flanked by Illumina standard adapter sequences. PCR was performed as 50 μL reactions containing 100 ng metagenomic DNA, dual-indexed forward and reverse primers (0.2 μM each), dNTPs (200 μM each), and Phusion high-fidelity DNA polymerase (1U, Thermo Fisher). Amplification parameters were 98°C(3 min) + [98°C(15 sec) + 50°C(30 sec) + 72°C(30 sec)] × 25 cycles +72°C(7 min).16 (link) Amplicon pools were combined then purified by addition of Axygen Axyprep MagPCR clean-up beads to an equal volume of 50 μL of amplicons and incubated for 15 min at room temperature. Products were washed multiple times with 80% ethanol and the pellet was resuspended in 32.5 μL EB buffer (Qiagen), incubated for 2 min at room temperature, and then placed on the magnetic stand for 5 min. The final amplicon pool was evaluated using an Advanced Analytical Fragment Analyzer automated electrophoresis system, quantified using quant-iT HS dsDNA reagent kits, and diluted according to the Illumina standard protocol for sequencing as 2 × 250 bp paired-end reads on the MiSeq instrument.
Gustafson K.L., McAdams Z.L., Russell A.L., Dorfmeyer R.A., Turner G.M, & Ericsson A.C. (2024). Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome. iScience, 27(3), 109090.
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