Agencourt ampure magnetic purification beads

Manufactured by Beckman Coulter

Sourced in United States

Agencourt AMPure magnetic purification beads are a product used for the purification of nucleic acids. The beads are designed to selectively bind DNA or RNA, allowing the removal of contaminants and unwanted components from sample preparations. This magnetic bead-based technology enables efficient and scalable purification of nucleic acids for various downstream applications.

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Lab products found in correlation

Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (3 mentions) Pacbio rs 2 platform, by Pacific Biosciences (1 mentions) Miseq sequencer, by Illumina (1 mentions) Qiaamp dna stool mini kit, by Qiagen (1 mentions)

2 protocols using agencourt ampure magnetic purification beads

Comprehensive Gut Microbiome Analysis

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Genomic DNA was isolated from frozen fecal samples using a DNA isolation kit (MoBio, Carlsbad, CA, United States) and quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, United States). 16S rRNA genes (V3-V4 region) were PCR amplified using the forward primer 341F (5′-ACTCCTACGGGRSGCAGCAG-3′) and reverse primer 806R (5′-GGACTACVVGGGTATCTAATC-3′), purified using Agencourt AMPure magnetic purification beads (Beckman Coulter, Brea, CA, United States), and run on 2% agarose gel. High-throughput sequencing of the PCR products was carried out on the PacBio RS II platform and analyzed at Ruiyi Biotechnology Co., Ltd. (Hangzhou, China).
Raw data from high-throughput sequencing were demultiplexed and quality filtered using the QIIME2 platform, then used to assemble operational taxonomic units (OTUs) to define species, genus, or class of bacterial communities by UCLUST algorithm (an exceptionally fast sequence clustering program for nucleotide and protein sequences) with a threshold of 97%. Principal component analysis (PCA) plots were generated using R software (v 4.1.2). STAMP (Ver. 2.1.3) software was applied to identify intestinal microbial phylotypes.

Cai S., Lin J., Li Z., Liu S., Feng Z., Zhang Y., Zhang Y., Huang J, & Chen Q. (2023). Alterations in intestinal microbiota and metabolites in individuals with Down syndrome and their correlation with inflammation and behavior disorders in mice. Frontiers in Microbiology, 14, 1016872.

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Fecal Microbiome 16S rRNA Sequencing

Cited 1 time

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Fecal microbial 16s rRNA was sequenced according to the protocol outlined in Chassaing et al. (2015).¹⁶ (link) Briefly, total bacterial DNA was isolated from feces using the QIAamp DNA Stool Mini Kit (Qiagen, Germantown, MD) according to manufacturer's instructions, and was stored at -80°C before further analysis. The 16S rRNA genes, region V4, were PCR amplified using the 515F/806R primer set (see Chassaing et al. [2015] for full sequence).¹⁶ (link) PCR reactions consisted of Hot Master PCR mix (Five Prime, San Francisco, CA), 0.2 μM of each primer, and 10–100 ng template. Reaction conditions were 3 minutes at 95°C, followed by 30 cycles of 45 seconds at 95°C, 60 seconds at 50°C and 90 seconds at 72°C on a Biorad thermocycler. PCR products were purified with Agencourt Ampure magnetic purification beads (Beckman Coulter, Indianapolis, IN). Sequencing was performed on an Illumina MiSeq sequencer (paired-end reads, 2 × 250 base pairs) at Cornell University, Ithaca.

Fields C.T., Chassaing B., Paul M.J., Gewirtz A.T, & de Vries G.J. (2017). Vasopressin deletion is associated with sex-specific shifts in the gut microbiome. Gut Microbes, 9(1), 13-25.

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