Agencourt ampure beads xp

Manufactured by Beckman Coulter

Sourced in United States

The Agencourt AMPure XP Beads are a magnetic bead-based solution for the purification and size selection of DNA, RNA, and proteins. The beads bind to the target molecules, allowing for efficient separation and removal of unwanted contaminants, salts, and free primers or nucleotides.

Automatically generated - may contain errors

Lab products found in correlation

Truseq small rna kit, by Illumina (2 mentions) Qiaquick gel extraction kit, by Qiagen (2 mentions) Miseq platform, by Illumina (1 mentions) Purelink microbiome dna purification kit, by Thermo Fisher Scientific (1 mentions) 2100 bioanalyzer, by Agilent Technologies (1 mentions) Nextflex 16s v4 amplicon seq kit, by PSC Biotech (1 mentions) Nextseq 550 sequencer, by Illumina (1 mentions) 2200 tapestation system, by Agilent Technologies (1 mentions) Qubit 3 fluorometer, by Thermo Fisher Scientific (1 mentions) Nextseq 500 550 high output kit v2, by Illumina (1 mentions) Nextera xt library prep kit, by Illumina (1 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions) Nextera xt index kit v2 set a, by Illumina (1 mentions) Gaiix, by Illumina (1 mentions) Hiseq 2000, by Illumina (1 mentions) Low range agarose, by Bio-Rad (1 mentions) Superscript 3, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

AMPure XP (483 citations) AMPure beads (406 citations) Agencourt AMPure XP (374 citations) Agencourt AMPure Beads (145 citations) Agencourt XP beads (18 citations) AMPure Beads XP (18 citations) Agencourt AMPure XP bead sizing (6 citations) Agencourt AMPure XP bead kit (6 citations) Agencourt AMPure XP Bead clean-up (2 citations) Agencourt AMPure XP bead solution (2 citations)

5 protocols using agencourt ampure beads xp

Comprehensive Microbiome DNA Profiling

Check if the same lab product or an alternative is used in the 5 most similar protocols

This was performed using the PureLink^TM Microbiome DNA Purification Kit from Thermofisher Scientific, USA, according to the manufacturer’s instructions. The DNA concentration was estimated by Nanodrop spectrophotometer.
The PCR cycling conditions followed those reported by Ramadan et al.15 (link) The V3-V4 regions of the 16S rRNA gene were amplified using the following primers with included Illumina adaptor, as follows:
Forward Primer.
5'TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG3'.
Reverse Primer.
5'GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTATCTAATCC'.
Validation of the size and quality of the amplified products was done using 1% agarose gel. Amplicons were purified by the Agencourt XP Ampure Beads (Beckman Coulter, USA). Finally, PCR amplicons of negative controls and fecal samples were sent to IGA Technology Services in Udine, Italy, where they were sequenced using the Illumina MiSeq platform (Illumina, USA).

Elsherbiny N.M., Ramadan M., Abu Faddan N.H., Hassan E.A., Ali M.E., Abd El-Rehim A.S., Abbas W.A., Abozaid M.A., Hassanin E., Mohamed G.A., Hetta H.F, & Salah M. (2022). Impact of Geographical Location on the Gut Microbiota Profile in Egyptian Children with Type 1 Diabetes Mellitus: A Pilot Study. International Journal of General Medicine, 15, 6173-6187.

+ Open protocol

+ Expand

16S rRNA Gene Amplification and Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

Illumina libraries were prepared following the protocol described by Dalmasso et al. (2016) with the NEXTflex 16S V4 Amplicon-Seq Kit (Bioo Scientific, Austin, USA). Briefly, the bacterial V4 region of the 16S ribosomal gene was amplified from 50 ng of DNA for each sample. The universal primers 515F and 806R tailed with Illumina barcoded adapters were used with the following touchdown PCR conditions: an initial 9 cycles (15 sec. at 95°C, 15 sec. at 68°C, 30 sec. at 72°C) and then another 23 cycles (15 sec. at 95°C, 15 sec. at 58°C, 30 sec. at 72°C). The PCR products were purified using Agencourt XP Ampure Beads (Beckman Coulter). The quality of the final products was assessed with a Bioanalyzer 2100 (Agilent Technologies).
The samples were quantified with Qubit (Invitrogen) and pooled in equal proportions for their paired-end sequencing with Illumina MiSeq for 312 cycles (150 cycles for each paired read and 12 cycles for the barcode sequence) at IGA Technology Services (Udine, Italy). To prevent focusing and phasing problems due to the sequencing of "low diversity" libraries, 30% PhiX genome was spiked in the pooled library.

Soto Del Rio M.L.D., Dalmasso A., Civera T, & Bottero M.T. (2017). Characterization of bacterial communities of donkey milk by high-throughput sequencing. International journal of food microbiology, 251.

+ Open protocol

+ Expand

Nextera XT Library Prep for RNA-seq

Check if the same lab product or an alternative is used in the 5 most similar protocols

Library preparation of suitable cDNAs were performed using Nextera^® XT Library Prep Kit (Illumina, CA) with Nextera^® XT Index Kit V2 Set A (Illumina, CA). Samples were normalized to 40 pg/μl for a total 200 pg input of amplified cDNA. The protocol was performed as described by the manufacturer. Libraries were purified with 0.6 x bead ratio using Agencourt AMPure beads XP (Beckman Coulter, IN) and eluted in 52.5 μl of elution buffer. Quality parameters as size (440 bp average) and concentration (1.03 ng/μl average) were measured using High Sensitivity D1000 ScreenTape and reagents run on 2200 TapeStation System (Agilent, CA) and Qubit™ dsDNA HS Assay Kit on a Qubit 3 Fluorometer (Thermo Fisher Scientific, MA), respectively. Good quality libraries were normalized to 1 nM. Thirteen samples were pooled to further perform 101 cycles of single read sequencing using a NextSeq^® 500/550 High Output Kit v2 (150 cycles) and NextSeq^® 550 sequencer (Illumina, CA). Sixty-two libraries with more than 20 million reads each were considered for analysis.

Zuccherato L.W., Machado C.M., Magalhães W.C., Martins P.R., Campos L.S., Braga L.C., Teixeira-Carvalho A., Martins-Filho O.A., Franco T.M., Paula S.O., da Silva I.T., Drummond R., Gollob K.J, & Salles P.G. (2021). Cervical Cancer Stem-Like Cell Transcriptome Profiles Predict Response to Chemoradiotherapy. Frontiers in Oncology, 11, 639339.

+ Open protocol

+ Expand

Enrichment of Primary RNA Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols

Depleted RNA samples were divided into two subsamples (hereby TAP+ and TAP-) containing the equivalent of 7.5 μg of total RNA and used for dRNA-seq library preparation as described [61 (link)]. The TAP+ subsample was pretreated with 10 U of Tobacco Acid Phosphatase (Tebu-Bio), the other steps being strictly run in parallel for the two subsamples. In brief, TAP treatment was followed by ligation with an excess of 5′ adapter (Illumina TruSeq Small RNA kit) and by reverse transcription using a random primer (RPO primer: 5′CCTTGGCACCCGAGAATTCCANNNNNN-3′). The first strand cDNA/RNA hybrids were then run on a 2% Low Range Agarose (Biorad). cDNAs ranging from 120 to 250 bp were extracted from a gel slice by using the Qiaquick gel extraction kit (Qiagen) and PCR amplified for 14 cycles using the Illumina primer RP1, and one of the indexed primers (Illumina TruSeq Small RNA kit). The resulting PCR products were purified with Agencourt AMPure Beads XP (Beckman) and sequenced on the Illumina GAIIX or HiSeq 2000.

Rosinski-Chupin I., Sauvage E., Sismeiro O., Villain A., Da Cunha V., Caliot M.E., Dillies M.A., Trieu-Cuot P., Bouloc P., Lartigue M.F, & Glaser P. (2015). Single nucleotide resolution RNA-seq uncovers new regulatory mechanisms in the opportunistic pathogen Streptococcus agalactiae. BMC Genomics, 16(1), 419.

+ Open protocol

+ Expand

RNA Library Preparation with TEX and TAP

Check if the same lab product or an alternative is used in the 5 most similar protocols

Two different treatments were combined: ± Terminator 5’-Phosphate-Dependent Exonuclease (TEX) [18 (link)] and ± Tobacco Acid Pyrophosphatase (TAP) [19 (link)]. Depleted RNA samples, containing the equivalent of 7 μg of total RNA, were denatured and treated with 1 unit of TEX (Epicentre) during 90 min at 30 °C and/or 10 units of TAP (Epicentre), for 1 h at 37 °C. Sample purification was performed using a phenol-chloroform extraction followed by an ethanol precipitation after each enzymatic treatment. Samples without TEX or TAP treatments underwent all the incubation and purification steps in parallel with the treated ones. All the samples were ligated with an excess of the 5′ adapter, 5′- GUU CAG AGU UCU ACA GUC CGA CGA UC – 3′ (Illumina TruSeq Small RNA kit). Reverse transcription was performed at 50 °C for 1 h using Superscript III (Invitrogen) and a random primer (RPO primer: 5′CCTTGGCACCCGAGAATTCCANNNNNN-3′). First strand cDNA/RNA hybrids were then run on a 2% Low Range Agarose gel (Biorad). cDNAs ranging from 200 to 400 bp were extracted from a gel slice using the Qiaquick gel extraction kit (Qiagen) and PCR amplified for 14 cycles using the Illumina primer RP1, and one of the indexed primers (Illumina TruSeq Small RNA kit). The resulting PCR products were purified with Agencourt AMPure Beads XP (Beckman).

Krin E., Pierlé S.A., Sismeiro O., Jagla B., Dillies M.A., Varet H., Irazoki O., Campoy S., Rouy Z., Cruveiller S., Médigue C., Coppée J.Y, & Mazel D. (2018). Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation. BMC Genomics, 19, 373.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!