ampure xp beads  (Beckman Coulter)


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  • 99
    Name:
    Agencourt AMPure XP SPRI beads
    Description:

    Catalog Number:
    A63880
    Price:
    None
    Score:
    85
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    Structured Review

    Beckman Coulter ampure xp beads
    cIAP1 is required for the recruitment of E2F1 onto chromatin. ChIP-seq analysis of the recruitment of E2F1 onto chromatin in HeLa cells transfected with scrambled (Sc) or cIAP1-siRNA. Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an ‘A’ base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bio Scientific) using the Bravo Platform (Agilent), size-selected after 4 cycles of <t>PCR</t> with <t>AMPure</t> XP beads (Beckman Coulter) and amplified by PCR for 10 more cycles (A). The efficiency of siRNA was checked by Western Blot analysis (B).

    https://www.bioz.com/result/ampure xp beads/product/Beckman Coulter
    Average 99 stars, based on 152 article reviews
    Price from $9.99 to $1999.99
    ampure xp beads - by Bioz Stars, 2019-10
    99/100 stars

    Images

    1) Product Images from "E2F1 binds to the peptide-binding groove within the BIR3 domain of cIAP1 and requires cIAP1 for chromatin binding"

    Article Title: E2F1 binds to the peptide-binding groove within the BIR3 domain of cIAP1 and requires cIAP1 for chromatin binding

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0206253

    cIAP1 is required for the recruitment of E2F1 onto chromatin. ChIP-seq analysis of the recruitment of E2F1 onto chromatin in HeLa cells transfected with scrambled (Sc) or cIAP1-siRNA. Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an ‘A’ base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bio Scientific) using the Bravo Platform (Agilent), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter) and amplified by PCR for 10 more cycles (A). The efficiency of siRNA was checked by Western Blot analysis (B).
    Figure Legend Snippet: cIAP1 is required for the recruitment of E2F1 onto chromatin. ChIP-seq analysis of the recruitment of E2F1 onto chromatin in HeLa cells transfected with scrambled (Sc) or cIAP1-siRNA. Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an ‘A’ base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bio Scientific) using the Bravo Platform (Agilent), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter) and amplified by PCR for 10 more cycles (A). The efficiency of siRNA was checked by Western Blot analysis (B).

    Techniques Used: Chromatin Immunoprecipitation, Transfection, Polymerase Chain Reaction, Amplification, Western Blot

    2) Product Images from "A comparative analysis of exome capture"

    Article Title: A comparative analysis of exome capture

    Journal: Genome Biology

    doi: 10.1186/gb-2011-12-9-r97

    Insert size distributions differed between the sample libraries prepared for the NimbleGen and Agilent exome capture kits . Sample libraries were produced independently and were prepared according to the manufacturer's guidelines. The insert size distributions were generated based on properly mapped and paired reads determined by our capture analysis pipeline. The NimbleGen library preparation process involved agarose gel electrophoresis-based size selection, whereas the Agilent process involved a more relaxed, bead-based size selection using AMPure XP (Beckman Coulter Genomics). Bead-based size selection is useful for removing DNA fragments smaller than 100 bp but less effective than gel-based size selection in producing narrow size distributions. Yet, from a technical standpoint, the gel-based process is more susceptible to variability of mean insert size. The two different size selection processes are illustrated by our group of NimbleGen capture libraries and our group of Agilent capture libraries. PDF, probability distribution function.
    Figure Legend Snippet: Insert size distributions differed between the sample libraries prepared for the NimbleGen and Agilent exome capture kits . Sample libraries were produced independently and were prepared according to the manufacturer's guidelines. The insert size distributions were generated based on properly mapped and paired reads determined by our capture analysis pipeline. The NimbleGen library preparation process involved agarose gel electrophoresis-based size selection, whereas the Agilent process involved a more relaxed, bead-based size selection using AMPure XP (Beckman Coulter Genomics). Bead-based size selection is useful for removing DNA fragments smaller than 100 bp but less effective than gel-based size selection in producing narrow size distributions. Yet, from a technical standpoint, the gel-based process is more susceptible to variability of mean insert size. The two different size selection processes are illustrated by our group of NimbleGen capture libraries and our group of Agilent capture libraries. PDF, probability distribution function.

    Techniques Used: Produced, Generated, Agarose Gel Electrophoresis, Electrophoresis, Selection

    Related Articles

    Cell Isolation:

    Article Title: PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
    Article Snippet: Paragraph title: Cell isolation and whole-genome amplification ... All amplified products were purified using Beckman Coulter’s Agencourt AMPure XP kit (cat no. A63880) immediately following the amplification reaction.

    Amplification:

    Article Title: Engineered CRISPR-Cas9 nucleases with altered PAM specificities
    Article Snippet: Genomic loci were amplified for a control condition (empty sgRNA), wild-type, and D1135E SpCas9. .. An Agencourt Ampure XP cleanup step (Beckman Coulter Genomics) was performed prior to pooling ~500 ng of DNA from each condition for library preparation.

    Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
    Article Snippet: Libraries were amplified using 13 cycles on the thermocycler. .. Post amplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. .. Libraries were validated using the Agilent High Sensitivity DNA Kit.

    Article Title: PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
    Article Snippet: We added 0.2 μl of SYBR green I (Life Technologies) into the reaction solution for real-time monitoring of the amplification. .. All amplified products were purified using Beckman Coulter’s Agencourt AMPure XP kit (cat no. A63880) immediately following the amplification reaction. .. To validate that the samples were thoroughly amplified, we used real-time whole-genome amplification monitoring and PCR validation with in-house designed 16-region primer panels (see Additional file : Table S1).

    Article Title: AAV vector-mediated in vivo reprogramming into pluripotency
    Article Snippet: Paragraph title: Non-restrictive linear amplification-mediated PCR (nrLAM-PCR) ... The rest was purified using the Agencourt AMPure XP PCR purification system (Beckman Coulter, Brea, CA, USA) following the manufacturer’s instructions.

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: Paragraph title: Amplicon library preparation and Oxford Nanopore sequencing ... This reaction mixture was then purified using Agencourt AMPure XP (Beckman Coulter Inc., cat. no. A63880) beads and washed and eluted in nanopore supplied reagents in 25 μL ultrapure water.

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, TX, USA) were performed using the GeneRead DNA Library I Core kit (Qiagen GmbH).

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Chromatin derived from 1.5×105 cells immunoprecipitated with specific Abs was eluted from the beads, treated with 1μg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously . .. ChIP-seq for H3K27me3 was performed as previously reported .

    Article Title: Diagnostic tools in the differential diagnosis of giant cell-rich lesions of bone at biopsy
    Article Snippet: The mutational status was analyzed by Sanger- and next generation amplicon based DNA sequencing (NGS). .. All purification and size selection steps were performed employing Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA).

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: The DNA obtained by ChIP was then amplified by 15 cycles of PCR with NEBNext Multiplex Oligos. .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1. .. The 'multiplexed' DNA libraries were sequenced on the Illumina HiSeq2000.

    Article Title: The balance of metagenomic elements shapes the skin microbiome in acne and health
    Article Snippet: Indexed libraries were amplified using the limited 12-cycle PCR program as instructed by the manufacturer’s guidelines. .. Libraries were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter).

    Article Title: Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium
    Article Snippet: In short, 10 ng of DNA per pool was amplified in 21 cycles by PCR using the Ion AmpliSeq™ mastermix, followed by barcode and adapter ligation. .. Amplified products were purified with Agencourt AMPure XP beads (Beckman Coulter Genomics, High Wycombe, UK). .. Emulsion PCR was performed using the Ion OneTouch™ 200 Template kit following the protocol of the Ion OneTouch™ System.

    Article Title: Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors
    Article Snippet: PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation. .. Sequencing data were base-called by sequencing software and analyzed by ABI Prism® SeqScape software.

    Article Title: Impact of Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza Responses
    Article Snippet: Bacterial 16S ribosomal RNA gene was amplified by using the 27F/534R primer set (27F 5′-AGAGTTTGATCCTGGCTCAG-3′, 534R 5′-ATTACCGCGGCTGCTGG-3′). .. PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) according to manufacturer’s protocol.

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water. .. The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water.

    Article Title: Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis
    Article Snippet: Illumina sequencing adaptors and index primers were added to the tagmented DNA via PCR amplification to generate a dual-indexed library for each sample. .. The DNA amplicon library was purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) to remove impurities such as free index primers, short DNA fragments, and enzymes. .. The cleaned DNA libraries were quantified using Qubit dsDNA HS Quantification kit and a Qubit 2.0 Fluorometer (Life Technologies) and normalised to 10 µL to form a pooled amplified library (PAL).

    Whole Genome Amplification:

    Article Title: PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
    Article Snippet: Paragraph title: Cell isolation and whole-genome amplification ... All amplified products were purified using Beckman Coulter’s Agencourt AMPure XP kit (cat no. A63880) immediately following the amplification reaction.

    Lambda DNA Preparation:

    Article Title: Improved data analysis for the MinION nanopore sequencer
    Article Snippet: For BAC DNA, sequencing libraries were prepared using unshared DNA as well as DNA sheared to an average length of 10 kb using g-TUBE (Covaris, Cat. No. 520079). .. Briefly, the DNA sample was spiked with ONT lambda DNA control, end-repaired using NEBNext End Repair Module (NEB, Cat. No. E6050S), and cleaned up using Agencourt AMPure XP beads (Beckman Coulter; Cat. No. A63880). .. The purified end-repaired DNA then underwent dA tailing using the NEB dA-Tailing Module (NEB, Cat. No. E6053S).

    Centrifugation:

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Chromatin was sheared using an AFA™ Focused-ultrasonicator (Covaris) for 15 min (duty cycle 2%, intensity 3, cycle/burst 200) and the sheared material was cleared by a 10 min centrifugation at 13,000 rpm at 4°C. .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously .

    Fluorescence In Situ Hybridization:

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: DNA was extracted from fin clip tissue punches in 96‐well format using a DNeasy 96 Blood & Tissue Kit (Qiagen, Inc., Valencia, CA). .. RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D. .. Etter, University of Oregon, personal communication ).

    Real-time Polymerase Chain Reaction:

    Article Title: Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis
    Article Snippet: The DNA amplicon library was purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) to remove impurities such as free index primers, short DNA fragments, and enzymes. .. The cleaned DNA libraries were quantified using Qubit dsDNA HS Quantification kit and a Qubit 2.0 Fluorometer (Life Technologies) and normalised to 10 µL to form a pooled amplified library (PAL).

    Incubation:

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: Briefly, immunoprecipitation reactions were performed with the above-indicated antibodies, each on approximately 500,000 cells, and incubated overnight at 4 °C. .. Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: The dA tailed amplicons were then adapter ligated in a total of 100 μL reaction volume and incubated at room temperature for 10 min. .. This reaction mixture was then purified using Agencourt AMPure XP (Beckman Coulter Inc., cat. no. A63880) beads and washed and eluted in nanopore supplied reagents in 25 μL ultrapure water.

    Genome Wide:

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: Paragraph title: Genome-wide ChIP-Seq analysis ... Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Modification:

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: ChIP DNA was prepared for high-throughput Illumina sequencing with a NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina kit (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers 1–12) according to a modified manufacturer's protocol. .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: DNA was extracted from fin clip tissue punches in 96‐well format using a DNeasy 96 Blood & Tissue Kit (Qiagen, Inc., Valencia, CA). .. RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D. .. Etter, University of Oregon, personal communication ).

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: The 16S rDNA amplicon pool was prepared according to the Lundberg et al. [ ] method with the following modification [ ]. .. The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water.

    Derivative Assay:

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Chromatin derived from 1.5×105 cells immunoprecipitated with specific Abs was eluted from the beads, treated with 1μg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously .

    Concentration Assay:

    Article Title: Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis
    Article Snippet: The DNA amplicon library was purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) to remove impurities such as free index primers, short DNA fragments, and enzymes. .. The cleaned DNA libraries were quantified using Qubit dsDNA HS Quantification kit and a Qubit 2.0 Fluorometer (Life Technologies) and normalised to 10 µL to form a pooled amplified library (PAL).

    Protease Inhibitor:

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Briefly, mTECs were cross-linked with 1% formaldehyde for 8 min, sorted and lysed for 10 min on ice in RadioImmunoPrecipitation Assay (RIPA) buffer [10mM Tris-HCl (pH 8.0), 1mM EDTA (pH 8.0), 140mM NaCl, 1% Triton X-100, 0.1% sodium dodecyl sulphate (SDS) and 0.1% sodium deoxycholate] supplemented with complete protease inhibitor cocktail (Roche). .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously .

    Genomic Sequencing:

    Article Title: The balance of metagenomic elements shapes the skin microbiome in acne and health
    Article Snippet: Genomic sequencing libraries were prepared using NexteraXT kit (Illumina). .. Libraries were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter).

    Transferring:

    Article Title: PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
    Article Snippet: All amplified products were purified using Beckman Coulter’s Agencourt AMPure XP kit (cat no. A63880) immediately following the amplification reaction. .. Most of the amplified products yielded more than 1 μg, and 800 ng was used for Illumina library construction.

    Infection:

    Article Title: Impact of Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza Responses
    Article Snippet: Fecal samples were collected between 6:00 a.m. and 7:00 a.m. in the morning each day beginning 3 days prior to infection (day −3) and stored at −80°C immediately after collection for microbiome analysis. .. PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) according to manufacturer’s protocol.

    Mutagenesis:

    Article Title: Engineered CRISPR-Cas9 nucleases with altered PAM specificities
    Article Snippet: Mutagenesis frequencies were quantified using a Qiaxcel capillary electrophoresis instrument (QIagen), as previously described for human cells and zebrafish . .. An Agencourt Ampure XP cleanup step (Beckman Coulter Genomics) was performed prior to pooling ~500 ng of DNA from each condition for library preparation.

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: In addition to KRAS mutation analysis by Sanger sequencing, samples with low tumor cell content were analyzed by more sensitive next-generation sequencing with the use of a Custom GeneRead DNASeq Panel (Qiagen GmbH, Hilden, Germany) consisting of 189 amplicons for mutation analysis of 19 cancer-related genes, (NRAS, H3F3A, RET, KRAS, AKT1, TP53, ERBB2, H3F3B, GNA11, ALK, GNAS, CTNNB1, PIK3CA, PDGFRA, KIT, EGFR, MET, BRAF, GNAQ ), according to the manufacturer’s protocol. .. An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA).

    DNA Sequencing:

    Article Title: Improved data analysis for the MinION nanopore sequencer
    Article Snippet: For BAC DNA, sequencing libraries were prepared using unshared DNA as well as DNA sheared to an average length of 10 kb using g-TUBE (Covaris, Cat. No. 520079). .. Briefly, the DNA sample was spiked with ONT lambda DNA control, end-repaired using NEBNext End Repair Module (NEB, Cat. No. E6050S), and cleaned up using Agencourt AMPure XP beads (Beckman Coulter; Cat. No. A63880).

    Article Title: Diagnostic tools in the differential diagnosis of giant cell-rich lesions of bone at biopsy
    Article Snippet: Paragraph title: DNA sequencing ... All purification and size selection steps were performed employing Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA).

    Article Title: Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors
    Article Snippet: Paragraph title: High-sensitivity and conventional sanger DNA sequencing ... PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation.

    Droplet Countercurrent Chromatography:

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). .. Phusion High-Fidelity DNA Polymerase (New England Biolabs) and TruSeq PCR Primers (Illumina, San Diego, CA) were used to amplify the libraries, which were then purified to remove adapter dimers using AMPure XP beads and multiplexed on the HiSeq 2000 (Illumina, San Diego, CA).

    Polymerase Chain Reaction:

    Article Title: Engineered CRISPR-Cas9 nucleases with altered PAM specificities
    Article Snippet: Roughly 200 ng of purified PCR product was denatured, annealed, and digested with T7E1 (New England BioLabs). .. An Agencourt Ampure XP cleanup step (Beckman Coulter Genomics) was performed prior to pooling ~500 ng of DNA from each condition for library preparation.

    Article Title: PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
    Article Snippet: The eight-strip PCR tube caps for the retrieval of cells were pre-exposed under O2 plasma for 30 s. The cells were lysed using proteinase K (cat no. P4850-1ML, Sigma Aldrich) according to the manufacturer’s directions after the PCR tubes were centrifuged. .. All amplified products were purified using Beckman Coulter’s Agencourt AMPure XP kit (cat no. A63880) immediately following the amplification reaction.

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). .. Barcoded immunoprecipitated DNA and input DNA were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (#E6240, New England Biolabs, Ipswich, MA) and TruSeq Adapters (Illumina) according to the manufacturer’s protocol on a SX-8G IP-STAR Compact Automated System (Diagenode).

    Article Title: AAV vector-mediated in vivo reprogramming into pluripotency
    Article Snippet: To rule out a contamination of the controls, a small fraction of the Mega PCR products were run on a 2% agarose gel. .. The rest was purified using the Agencourt AMPure XP PCR purification system (Beckman Coulter, Brea, CA, USA) following the manufacturer’s instructions. .. In total 50 ng of each sample were pooled and sequenced on a MiSeq Illumina platform at the Deep Sequencing Core Facility of the German Cancer Research Center (Heidelberg, Germany).

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: In brief, genomic DNA was quantified and target enrichment was processed with the GeneRead DNAseq Panel PCR V2 kit (Qiagen GmbH) applying 40 ng genomic DNA quantified with a Qubit® dsDNA HS kit and a Qubit® 2.0 Fluorometer (Life Technologies; Thermo Fisher Scientific, Inc.). .. An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA).

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Chromatin derived from 1.5×105 cells immunoprecipitated with specific Abs was eluted from the beads, treated with 1μg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously . .. ChIP-seq for H3K27me3 was performed as previously reported .

    Article Title: Diagnostic tools in the differential diagnosis of giant cell-rich lesions of bone at biopsy
    Article Snippet: Target enrichment was processed by means of the GeneRead DNAseq Panel PCR V2 Kit (Qiagen, Hilden, Germany), following the manufacturer’s instructions. .. All purification and size selection steps were performed employing Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA).

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: The DNA obtained by ChIP was then amplified by 15 cycles of PCR with NEBNext Multiplex Oligos. .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Article Title: The balance of metagenomic elements shapes the skin microbiome in acne and health
    Article Snippet: Indexed libraries were amplified using the limited 12-cycle PCR program as instructed by the manufacturer’s guidelines. .. Libraries were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter).

    Article Title: Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium
    Article Snippet: In short, 10 ng of DNA per pool was amplified in 21 cycles by PCR using the Ion AmpliSeq™ mastermix, followed by barcode and adapter ligation. .. Amplified products were purified with Agencourt AMPure XP beads (Beckman Coulter Genomics, High Wycombe, UK).

    Article Title: Construction of a High-Density Genetic Map and Identification of Loci Related to Hollow Stem Trait in Broccoli (Brassic oleracea L. italica)
    Article Snippet: Polymerase chain reaction (PCR) was carried out using dNTP, diluted digestion-ligation DNA samples, Q5® High-Fidelity DNA Polymerase and PCR primers (Forward primer: 5′- AATGATACGGCGACCACCGA-3′, reverse primer: 5′-CAAGCAGAAGACGGCATACG-3′). .. Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled. .. Pooled samples were separated by 2% agarose gel electrophoresis.

    Article Title: Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors
    Article Snippet: All reactions were subjected to identical thermocycler settings; initial denaturation at 95°C for 6 minutes; 40 cycles of denaturation at 95°C for 30 seconds, primer annealing at 56°C for 30 seconds, and extension at 72°C for 1 minute 20 seconds; this was followed by a final extension at 72°C for 10 minutes. .. PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation. .. The precipitated DNA was then resuspended in 10 μL Hi-Di Formamide (Life Technologies; Waltham, MA, U.S.A.), denatured at 95°C for 3 minutes, and run on the ABI 3730XL sequencer.

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: DNA was extracted from fin clip tissue punches in 96‐well format using a DNeasy 96 Blood & Tissue Kit (Qiagen, Inc., Valencia, CA). .. RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D. .. Etter, University of Oregon, personal communication ).

    Article Title: Impact of Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza Responses
    Article Snippet: PCR reactions were performed using phusion high-fidelity PCR Mastermix (Invitrogen, Carlsbad, CA, USA) with the following condition: 95°C for 2 min (1 cycle), 95°C for 20 s/56°C for 30 s/72°C for 1 min (30 cycles). .. PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) according to manufacturer’s protocol. .. Library was prepared with Illumina’s instruction specifically for Miseq platform.

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water. .. Because the “universal” primer 515F does not effectively amplify several groups of Archaea and Bacteria, we supplemented it with modified versions that included 10% 515FArch (5′ GTGKCAGCMGCCGCGGTAA) and 3% TM7 (5′ GTGCCAGCMGCCGCGGTCA).

    Article Title: Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis
    Article Snippet: Illumina sequencing adaptors and index primers were added to the tagmented DNA via PCR amplification to generate a dual-indexed library for each sample. .. The DNA amplicon library was purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) to remove impurities such as free index primers, short DNA fragments, and enzymes.

    Sonication:

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: Lysates were sonicated in an E220 focused-ultrasonicator (Covaris, Woburn, MA) to a desired fragment size distribution of 100–500 base pairs. .. Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

    ChIP-sequencing:

    Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
    Article Snippet: ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. .. Post amplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter.

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: Paragraph title: ChIP-seq and motif analysis ... Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Chromatin derived from 1.5×105 cells immunoprecipitated with specific Abs was eluted from the beads, treated with 1μg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously . .. ChIP-seq for H3K27me3 was performed as previously reported .

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: Paragraph title: Genome-wide ChIP-Seq analysis ... Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    DNA Extraction:

    Article Title: Impact of Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza Responses
    Article Snippet: Total DNA was extracted from fecal samples by using Power Soil DNA Extraction kit (Mo Bio Laboratories, Carlsbad, CA, USA) per manufacturer’s protocol. .. PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) according to manufacturer’s protocol.

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: Paragraph title: DNA isolation and 16S rDNA sequencing ... The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water.

    RNA Sequencing Assay:

    Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
    Article Snippet: Post amplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. .. Post amplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter.

    Fluorescence:

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D. .. RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D.

    Magnetic Beads:

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: The immune complex was collected with protein A/G agarose or magnetic beads and washed sequentially in the low salt wash buffer (20 mM Tris pH8, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), the high salt wash buffer (20 mM Tris pH8, 500 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), the LiCl wash buffer (10 mM Tris pH8, 250 mM LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA) and TE. .. Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: In brief, genomic DNA was quantified and target enrichment was processed with the GeneRead DNAseq Panel PCR V2 kit (Qiagen GmbH) applying 40 ng genomic DNA quantified with a Qubit® dsDNA HS kit and a Qubit® 2.0 Fluorometer (Life Technologies; Thermo Fisher Scientific, Inc.). .. An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, TX, USA) were performed using the GeneRead DNA Library I Core kit (Qiagen GmbH).

    Article Title: Diagnostic tools in the differential diagnosis of giant cell-rich lesions of bone at biopsy
    Article Snippet: Target enrichment was processed by means of the GeneRead DNAseq Panel PCR V2 Kit (Qiagen, Hilden, Germany), following the manufacturer’s instructions. .. All purification and size selection steps were performed employing Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, Texas, USA) were conducted using the GeneRead DNA Library I Core Kit (Qiagen, Hilden, Germany).

    Article Title: The balance of metagenomic elements shapes the skin microbiome in acne and health
    Article Snippet: Indexed libraries were amplified using the limited 12-cycle PCR program as instructed by the manufacturer’s guidelines. .. Libraries were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter). .. Library quality and average fragment length were assessed using Bioanalyzer (Agilent Technologies).

    Article Title: Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors
    Article Snippet: All reactions were subjected to identical thermocycler settings; initial denaturation at 95°C for 6 minutes; 40 cycles of denaturation at 95°C for 30 seconds, primer annealing at 56°C for 30 seconds, and extension at 72°C for 1 minute 20 seconds; this was followed by a final extension at 72°C for 10 minutes. .. PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation. .. The precipitated DNA was then resuspended in 10 μL Hi-Di Formamide (Life Technologies; Waltham, MA, U.S.A.), denatured at 95°C for 3 minutes, and run on the ABI 3730XL sequencer.

    Multiple Displacement Amplification:

    Article Title: PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
    Article Snippet: For whole-genome amplification by multiple displacement amplification, we used GE’s Illustra Genomiphi V2 DNA amplification kit (cat no. 25-6600-30). .. All amplified products were purified using Beckman Coulter’s Agencourt AMPure XP kit (cat no. A63880) immediately following the amplification reaction.

    Isolation:

    Article Title: Identification of differentially expressed non-coding RNAs and mRNAs involved in Qi stagnation and blood stasis syndrome
    Article Snippet: Paragraph title: RNA isolation and library preparation ... RNA purity was confirmed using the Agencourt AMPure XP (cat. no. A63881; Beckman Coulter, Brea, CA, USA).

    Article Title: Improved data analysis for the MinION nanopore sequencer
    Article Snippet: Briefly, the DNA sample was spiked with ONT lambda DNA control, end-repaired using NEBNext End Repair Module (NEB, Cat. No. E6050S), and cleaned up using Agencourt AMPure XP beads (Beckman Coulter; Cat. No. A63880). .. This was followed by ligation of ONT sequencing adaptors (adaptor Mix and HP adaptor) using Blunt/TA Ligase Master Mix (NEB, Cat. No. M0367S).

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: DNA was isolated from pelleted microbial cells, without separation of residual biomass, using the PowerLyzer Powersoil DNA Isolation kit from MoBio Laboratories Inc. (Carlsbad, CA) following the manufacturer’s protocol as has previously been used to investigate methanoarchaea in environmental and anaerobic digester communities [ ]. .. The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water.

    Size-exclusion Chromatography:

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: In brief, genomic DNA was quantified and target enrichment was processed with the GeneRead DNAseq Panel PCR V2 kit (Qiagen GmbH) applying 40 ng genomic DNA quantified with a Qubit® dsDNA HS kit and a Qubit® 2.0 Fluorometer (Life Technologies; Thermo Fisher Scientific, Inc.). .. An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, TX, USA) were performed using the GeneRead DNA Library I Core kit (Qiagen GmbH).

    Purification:

    Article Title: Engineered CRISPR-Cas9 nucleases with altered PAM specificities
    Article Snippet: Roughly 200 ng of purified PCR product was denatured, annealed, and digested with T7E1 (New England BioLabs). .. An Agencourt Ampure XP cleanup step (Beckman Coulter Genomics) was performed prior to pooling ~500 ng of DNA from each condition for library preparation.

    Article Title: PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
    Article Snippet: We added 0.2 μl of SYBR green I (Life Technologies) into the reaction solution for real-time monitoring of the amplification. .. All amplified products were purified using Beckman Coulter’s Agencourt AMPure XP kit (cat no. A63880) immediately following the amplification reaction. .. To validate that the samples were thoroughly amplified, we used real-time whole-genome amplification monitoring and PCR validation with in-house designed 16-region primer panels (see Additional file : Table S1).

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: The immune complex was collected with protein A/G agarose or magnetic beads and washed sequentially in the low salt wash buffer (20 mM Tris pH8, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), the high salt wash buffer (20 mM Tris pH8, 500 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), the LiCl wash buffer (10 mM Tris pH8, 250 mM LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA) and TE. .. Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA). .. Barcoded immunoprecipitated DNA and input DNA were prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (#E6240, New England Biolabs, Ipswich, MA) and TruSeq Adapters (Illumina) according to the manufacturer’s protocol on a SX-8G IP-STAR Compact Automated System (Diagenode).

    Article Title: AAV vector-mediated in vivo reprogramming into pluripotency
    Article Snippet: To rule out a contamination of the controls, a small fraction of the Mega PCR products were run on a 2% agarose gel. .. The rest was purified using the Agencourt AMPure XP PCR purification system (Beckman Coulter, Brea, CA, USA) following the manufacturer’s instructions. .. In total 50 ng of each sample were pooled and sequenced on a MiSeq Illumina platform at the Deep Sequencing Core Facility of the German Cancer Research Center (Heidelberg, Germany).

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: The dA tailed amplicons were then adapter ligated in a total of 100 μL reaction volume and incubated at room temperature for 10 min. .. This reaction mixture was then purified using Agencourt AMPure XP (Beckman Coulter Inc., cat. no. A63880) beads and washed and eluted in nanopore supplied reagents in 25 μL ultrapure water. .. This pre-sequencing mix was added with the fuel mix and EP buffer and loaded on the R7.3 flow cell and sequenced.

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: In brief, genomic DNA was quantified and target enrichment was processed with the GeneRead DNAseq Panel PCR V2 kit (Qiagen GmbH) applying 40 ng genomic DNA quantified with a Qubit® dsDNA HS kit and a Qubit® 2.0 Fluorometer (Life Technologies; Thermo Fisher Scientific, Inc.). .. An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, TX, USA) were performed using the GeneRead DNA Library I Core kit (Qiagen GmbH).

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Chromatin derived from 1.5×105 cells immunoprecipitated with specific Abs was eluted from the beads, treated with 1μg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously . .. ChIP-seq for H3K27me3 was performed as previously reported .

    Article Title: Diagnostic tools in the differential diagnosis of giant cell-rich lesions of bone at biopsy
    Article Snippet: Target enrichment was processed by means of the GeneRead DNAseq Panel PCR V2 Kit (Qiagen, Hilden, Germany), following the manufacturer’s instructions. .. All purification and size selection steps were performed employing Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, Texas, USA) were conducted using the GeneRead DNA Library I Core Kit (Qiagen, Hilden, Germany).

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: The DNA obtained by ChIP was then amplified by 15 cycles of PCR with NEBNext Multiplex Oligos. .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1. .. The 'multiplexed' DNA libraries were sequenced on the Illumina HiSeq2000.

    Article Title: The balance of metagenomic elements shapes the skin microbiome in acne and health
    Article Snippet: Indexed libraries were amplified using the limited 12-cycle PCR program as instructed by the manufacturer’s guidelines. .. Libraries were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter). .. Library quality and average fragment length were assessed using Bioanalyzer (Agilent Technologies).

    Article Title: Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium
    Article Snippet: In short, 10 ng of DNA per pool was amplified in 21 cycles by PCR using the Ion AmpliSeq™ mastermix, followed by barcode and adapter ligation. .. Amplified products were purified with Agencourt AMPure XP beads (Beckman Coulter Genomics, High Wycombe, UK). .. Emulsion PCR was performed using the Ion OneTouch™ 200 Template kit following the protocol of the Ion OneTouch™ System.

    Article Title: Construction of a High-Density Genetic Map and Identification of Loci Related to Hollow Stem Trait in Broccoli (Brassic oleracea L. italica)
    Article Snippet: Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled. .. Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled.

    Article Title: Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors
    Article Snippet: All reactions were subjected to identical thermocycler settings; initial denaturation at 95°C for 6 minutes; 40 cycles of denaturation at 95°C for 30 seconds, primer annealing at 56°C for 30 seconds, and extension at 72°C for 1 minute 20 seconds; this was followed by a final extension at 72°C for 10 minutes. .. PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation. .. The precipitated DNA was then resuspended in 10 μL Hi-Di Formamide (Life Technologies; Waltham, MA, U.S.A.), denatured at 95°C for 3 minutes, and run on the ABI 3730XL sequencer.

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: DNA was extracted from fin clip tissue punches in 96‐well format using a DNeasy 96 Blood & Tissue Kit (Qiagen, Inc., Valencia, CA). .. RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D. .. Etter, University of Oregon, personal communication ).

    Article Title: Impact of Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza Responses
    Article Snippet: PCR reactions were performed using phusion high-fidelity PCR Mastermix (Invitrogen, Carlsbad, CA, USA) with the following condition: 95°C for 2 min (1 cycle), 95°C for 20 s/56°C for 30 s/72°C for 1 min (30 cycles). .. PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) according to manufacturer’s protocol. .. Library was prepared with Illumina’s instruction specifically for Miseq platform.

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: For template tagging, 5 cycles of amplification were performed by denaturing the reaction at 95 °C for 1 min, annealing at 50 °C for 2 min, extension at 72 °C for 2 min and cooled down to 4 °C. .. The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water. .. The primers for tagging were a mixture of 515F (5′ GTGCCAGCMGCCGCGGTAA) and 806R (5′ GGACTACHVGGGTWTCTAA) for 16S rDNA V4 region.

    Article Title: Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis
    Article Snippet: Illumina sequencing adaptors and index primers were added to the tagmented DNA via PCR amplification to generate a dual-indexed library for each sample. .. The DNA amplicon library was purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) to remove impurities such as free index primers, short DNA fragments, and enzymes. .. The cleaned DNA libraries were quantified using Qubit dsDNA HS Quantification kit and a Qubit 2.0 Fluorometer (Life Technologies) and normalised to 10 µL to form a pooled amplified library (PAL).

    Sequencing:

    Article Title: Engineered CRISPR-Cas9 nucleases with altered PAM specificities
    Article Snippet: An Agencourt Ampure XP cleanup step (Beckman Coulter Genomics) was performed prior to pooling ~500 ng of DNA from each condition for library preparation. .. Dual-indexed Tru-Seq Illumina deep-sequencing libraries were generated using the KAPA HTP library preparation kit (KAPA BioSystems).

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: The library preparation for amplicon sequencing was done using SQK-MAP003 following manufacturer’s protocol (ONT). .. This reaction mixture was then purified using Agencourt AMPure XP (Beckman Coulter Inc., cat. no. A63880) beads and washed and eluted in nanopore supplied reagents in 25 μL ultrapure water.

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: In addition to KRAS mutation analysis by Sanger sequencing, samples with low tumor cell content were analyzed by more sensitive next-generation sequencing with the use of a Custom GeneRead DNASeq Panel (Qiagen GmbH, Hilden, Germany) consisting of 189 amplicons for mutation analysis of 19 cancer-related genes, (NRAS, H3F3A, RET, KRAS, AKT1, TP53, ERBB2, H3F3B, GNA11, ALK, GNAS, CTNNB1, PIK3CA, PDGFRA, KIT, EGFR, MET, BRAF, GNAQ ), according to the manufacturer’s protocol. .. An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA).

    Article Title: Improved data analysis for the MinION nanopore sequencer
    Article Snippet: Paragraph title: M13 MinION sequencing ... Briefly, the DNA sample was spiked with ONT lambda DNA control, end-repaired using NEBNext End Repair Module (NEB, Cat. No. E6050S), and cleaned up using Agencourt AMPure XP beads (Beckman Coulter; Cat. No. A63880).

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: ChIP DNA was prepared for high-throughput Illumina sequencing with a NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina kit (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers 1–12) according to a modified manufacturer's protocol. .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Article Title: The balance of metagenomic elements shapes the skin microbiome in acne and health
    Article Snippet: Libraries were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter). .. Finally, libraries were randomly pooled together and sequenced using MiSeq and/or HiSeq platforms (Illumina) with paired-end reads of 251 bp or 101 bp, respectively.

    Article Title: Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium
    Article Snippet: Paragraph title: AmpliSeq enrichment and Ion Torrent sequencing ... Amplified products were purified with Agencourt AMPure XP beads (Beckman Coulter Genomics, High Wycombe, UK).

    Article Title: Construction of a High-Density Genetic Map and Identification of Loci Related to Hollow Stem Trait in Broccoli (Brassic oleracea L. italica)
    Article Snippet: Paragraph title: SLAF Library Construction and High-Throughput Sequencing ... Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled.

    Article Title: Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors
    Article Snippet: All reactions were subjected to identical thermocycler settings; initial denaturation at 95°C for 6 minutes; 40 cycles of denaturation at 95°C for 30 seconds, primer annealing at 56°C for 30 seconds, and extension at 72°C for 1 minute 20 seconds; this was followed by a final extension at 72°C for 10 minutes. .. PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation. .. The precipitated DNA was then resuspended in 10 μL Hi-Di Formamide (Life Technologies; Waltham, MA, U.S.A.), denatured at 95°C for 3 minutes, and run on the ABI 3730XL sequencer.

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: Paragraph title: Sample collection and RAD sequencing ... RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D.

    Article Title: Impact of Age, Caloric Restriction, and Influenza Infection on Mouse Gut Microbiome: An Exploratory Study of the Role of Age-Related Microbiome Changes on Influenza Responses
    Article Snippet: PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) according to manufacturer’s protocol. .. PCR products were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) according to manufacturer’s protocol.

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: Paragraph title: DNA isolation and 16S rDNA sequencing ... The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water.

    Article Title: Emergence of Vancomycin-Resistant Enterococcus faecium at an Australian Hospital: A Whole Genome Sequencing Analysis
    Article Snippet: Paragraph title: DNA library preparation and whole-genome sequencing ... The DNA amplicon library was purified with Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) to remove impurities such as free index primers, short DNA fragments, and enzymes.

    Immunoprecipitation:

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: Briefly, immunoprecipitation reactions were performed with the above-indicated antibodies, each on approximately 500,000 cells, and incubated overnight at 4 °C. .. Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Chromatin derived from 1.5×105 cells immunoprecipitated with specific Abs was eluted from the beads, treated with 1μg DNase-free RNase (Roche) for 30 min at 37°C and with Proteinase K (Roche) for 2 hrs at 37°C followed by reverse cross-linking by leaving the plate at 65°C overnight. .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously .

    Polyacrylamide Gel Electrophoresis:

    Article Title: Construction of a High-Density Genetic Map and Identification of Loci Related to Hollow Stem Trait in Broccoli (Brassic oleracea L. italica)
    Article Snippet: Subsequently, the A-tailed fragments were connected to duplex tag-labeled sequencing adapters (PAGE-purified, Life Technologies, United States) by T4 DNA ligase. .. Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled.

    Lysis:

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: Briefly, cells were fixed in a 1% methanol-free formaldehyde solution and then resuspended in sodium dodecyl sulfate (SDS) lysis buffer. .. Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

    Sample Prep:

    Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
    Article Snippet: Paragraph title: NGS Sample Preparation ... Post amplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter.

    Shotgun Sequencing:

    Article Title: The balance of metagenomic elements shapes the skin microbiome in acne and health
    Article Snippet: Paragraph title: Library construction and metagenomic shotgun sequencing ... Libraries were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter).

    Mouse Assay:

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: 1.5 × 105 mTEChi from 4–6-week-old female B6 mice were used for each ChIP-seq sample, adapting published protocols , . .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously .

    Chromatin Immunoprecipitation:

    Article Title: Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL
    Article Snippet: ChIP assays were processed on a SX-8G IP-STAR Compact Automated System (Diagenode, Denville, NJ) using a direct ChIP protocol . .. Chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3), and then reverse cross-linked with 0.2 M NaCl at 65 °C for 4 h. DNA fragments were purified using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA).

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: The DNA obtained by ChIP was then amplified by 15 cycles of PCR with NEBNext Multiplex Oligos. .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Article Title: Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium
    Article Snippet: Amplified products were purified with Agencourt AMPure XP beads (Beckman Coulter Genomics, High Wycombe, UK). .. Amplified products were purified with Agencourt AMPure XP beads (Beckman Coulter Genomics, High Wycombe, UK).

    RNA Extraction:

    Article Title: Identification of differentially expressed non-coding RNAs and mRNAs involved in Qi stagnation and blood stasis syndrome
    Article Snippet: RNA purity was confirmed using the Agencourt AMPure XP (cat. no. A63881; Beckman Coulter, Brea, CA, USA). .. RNA purity was confirmed using the Agencourt AMPure XP (cat. no. A63881; Beckman Coulter, Brea, CA, USA).

    Software:

    Article Title: Diagnostic tools in the differential diagnosis of giant cell-rich lesions of bone at biopsy
    Article Snippet: All purification and size selection steps were performed employing Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA). .. NGS was performed applying 12.5 pM library pools (2% PhiX V3 control) and the MiSeq Reagent v2 chemistry (Illumina, San Diego, CA, USA).

    Article Title: Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors
    Article Snippet: PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation. .. PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation.

    SYBR Green Assay:

    Article Title: PHLI-seq: constructing and visualizing cancer genomic maps in 3D by phenotype-based high-throughput laser-aided isolation and sequencing
    Article Snippet: We added 0.2 μl of SYBR green I (Life Technologies) into the reaction solution for real-time monitoring of the amplification. .. All amplified products were purified using Beckman Coulter’s Agencourt AMPure XP kit (cat no. A63880) immediately following the amplification reaction.

    Multiplex Assay:

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: The DNA obtained by ChIP was then amplified by 15 cycles of PCR with NEBNext Multiplex Oligos. .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Selection:

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: In brief, genomic DNA was quantified and target enrichment was processed with the GeneRead DNAseq Panel PCR V2 kit (Qiagen GmbH) applying 40 ng genomic DNA quantified with a Qubit® dsDNA HS kit and a Qubit® 2.0 Fluorometer (Life Technologies; Thermo Fisher Scientific, Inc.). .. An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, TX, USA) were performed using the GeneRead DNA Library I Core kit (Qiagen GmbH).

    Article Title: Diagnostic tools in the differential diagnosis of giant cell-rich lesions of bone at biopsy
    Article Snippet: Target enrichment was processed by means of the GeneRead DNAseq Panel PCR V2 Kit (Qiagen, Hilden, Germany), following the manufacturer’s instructions. .. All purification and size selection steps were performed employing Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, Texas, USA) were conducted using the GeneRead DNA Library I Core Kit (Qiagen, Hilden, Germany).

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: DNA fragments 150–600 bp in length were then selected with Pippin Prep 2% Agarose Gel Cassettes and the Pippin Prep DNA Size Selection System (Sage Science). .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: DNA was extracted from fin clip tissue punches in 96‐well format using a DNeasy 96 Blood & Tissue Kit (Qiagen, Inc., Valencia, CA). .. RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D. .. Etter, University of Oregon, personal communication ).

    Agarose Gel Electrophoresis:

    Article Title: AAV vector-mediated in vivo reprogramming into pluripotency
    Article Snippet: To rule out a contamination of the controls, a small fraction of the Mega PCR products were run on a 2% agarose gel. .. The rest was purified using the Agencourt AMPure XP PCR purification system (Beckman Coulter, Brea, CA, USA) following the manufacturer’s instructions.

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: DNA fragments 150–600 bp in length were then selected with Pippin Prep 2% Agarose Gel Cassettes and the Pippin Prep DNA Size Selection System (Sage Science). .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: DNA was eluted in 100 μL of water and quality/quantity was assessed by Nanodrop analysis (Thermo Scientific, Wilmington, DE) and on a 1% agarose gel. .. The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water.

    Radio Immunoprecipitation:

    Article Title: The transcriptional regulator Aire binds to and activates super-enhancers
    Article Snippet: Briefly, mTECs were cross-linked with 1% formaldehyde for 8 min, sorted and lysed for 10 min on ice in RadioImmunoPrecipitation Assay (RIPA) buffer [10mM Tris-HCl (pH 8.0), 1mM EDTA (pH 8.0), 140mM NaCl, 1% Triton X-100, 0.1% sodium dodecyl sulphate (SDS) and 0.1% sodium deoxycholate] supplemented with complete protease inhibitor cocktail (Roche). .. DNA from reverse cross-linked material was purified with SPRI beads (Agencourt AMPure XP beads, Beckman Coulter); and sequential steps of end-repair, A-base addition, adaptor-ligation and PCR amplification (15 cycles) were performed to prepare the ChIP-seq library for each sample, as described previously .

    Electrophoresis:

    Article Title: Engineered CRISPR-Cas9 nucleases with altered PAM specificities
    Article Snippet: Mutagenesis frequencies were quantified using a Qiaxcel capillary electrophoresis instrument (QIagen), as previously described for human cells and zebrafish . .. An Agencourt Ampure XP cleanup step (Beckman Coulter Genomics) was performed prior to pooling ~500 ng of DNA from each condition for library preparation.

    Ethanol Precipitation:

    Article Title: Using high-sensitivity sequencing for the detection of mutations in BTK and PLCγ2 genes in cellular and cell-free DNA and correlation with progression in patients treated with BTK inhibitors
    Article Snippet: All reactions were subjected to identical thermocycler settings; initial denaturation at 95°C for 6 minutes; 40 cycles of denaturation at 95°C for 30 seconds, primer annealing at 56°C for 30 seconds, and extension at 72°C for 1 minute 20 seconds; this was followed by a final extension at 72°C for 10 minutes. .. PCR products were purified using Agencourt AMPure XP magnetic beads (Beckman Coulter; Brea, CA, U.S.A.), bi-directionally sequenced using a BigDye Terminator v3.1 Cycle sequencing kit (Life Technologies; Waltham, MA, U.S.A.), and subjected to ethanol precipitation. .. The precipitated DNA was then resuspended in 10 μL Hi-Di Formamide (Life Technologies; Waltham, MA, U.S.A.), denatured at 95°C for 3 minutes, and run on the ABI 3730XL sequencer.

    Next-Generation Sequencing:

    Article Title: Resetting the Epigenetic Balance of Polycomb and COMPASS Function at Enhancers for Cancer Therapy
    Article Snippet: Paragraph title: NGS Sample Preparation ... Post amplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter.

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: Paragraph title: Next-generation sequencing ... An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA).

    Article Title: Diagnostic tools in the differential diagnosis of giant cell-rich lesions of bone at biopsy
    Article Snippet: The mutational status was analyzed by Sanger- and next generation amplicon based DNA sequencing (NGS). .. All purification and size selection steps were performed employing Agencourt AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA).

    Ligation:

    Article Title: Improved data analysis for the MinION nanopore sequencer
    Article Snippet: Briefly, the DNA sample was spiked with ONT lambda DNA control, end-repaired using NEBNext End Repair Module (NEB, Cat. No. E6050S), and cleaned up using Agencourt AMPure XP beads (Beckman Coulter; Cat. No. A63880). .. The purified end-repaired DNA then underwent dA tailing using the NEB dA-Tailing Module (NEB, Cat. No. E6053S).

    Article Title: Development of a semi-conductor sequencing-based panel for genotyping of colon and lung cancer by the Onconetwork consortium
    Article Snippet: In short, 10 ng of DNA per pool was amplified in 21 cycles by PCR using the Ion AmpliSeq™ mastermix, followed by barcode and adapter ligation. .. Amplified products were purified with Agencourt AMPure XP beads (Beckman Coulter Genomics, High Wycombe, UK).

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: DNA was extracted from fin clip tissue punches in 96‐well format using a DNeasy 96 Blood & Tissue Kit (Qiagen, Inc., Valencia, CA). .. RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D. .. Etter, University of Oregon, personal communication ).

    Activation Assay:

    Article Title: Expression levels of hnRNP K and p21WAF1/CIP1 are associated with resistance to radiochemotherapy independent of p53 pathway activation in rectal adenocarcinoma
    Article Snippet: In brief, genomic DNA was quantified and target enrichment was processed with the GeneRead DNAseq Panel PCR V2 kit (Qiagen GmbH) applying 40 ng genomic DNA quantified with a Qubit® dsDNA HS kit and a Qubit® 2.0 Fluorometer (Life Technologies; Thermo Fisher Scientific, Inc.). .. An initial activation step (95°C; 15 min) was followed by 25 cycles of denaturing at 95°C (15 sec) and annealing at 60°C (4 min), followed by extension at 72°C for 10 min. All purification and size selection steps were performed using Agencourt AMPure XP magnetic beads (Beckman Coulter, Inc., Brea, CA, USA). .. End repair, A-addition and ligation to NEXTflex-96 DNA barcodes (Bioo Scientific, Austin, TX, USA) were performed using the GeneRead DNA Library I Core kit (Qiagen GmbH).

    BAC Assay:

    Article Title: Improved data analysis for the MinION nanopore sequencer
    Article Snippet: For BAC DNA, sequencing libraries were prepared using unshared DNA as well as DNA sheared to an average length of 10 kb using g-TUBE (Covaris, Cat. No. 520079). .. Briefly, the DNA sample was spiked with ONT lambda DNA control, end-repaired using NEBNext End Repair Module (NEB, Cat. No. E6050S), and cleaned up using Agencourt AMPure XP beads (Beckman Coulter; Cat. No. A63880).

    High Throughput Screening Assay:

    Article Title: The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells
    Article Snippet: ChIP DNA was prepared for high-throughput Illumina sequencing with a NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina kit (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers 1–12) according to a modified manufacturer's protocol. .. Amplified DNA was purified with DNA to Agencourt AMPure XP beads (Beckman Coulter) in a ratio of 1:1.

    Article Title: Construction of a High-Density Genetic Map and Identification of Loci Related to Hollow Stem Trait in Broccoli (Brassic oleracea L. italica)
    Article Snippet: Paragraph title: SLAF Library Construction and High-Throughput Sequencing ... Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled.

    Article Title: Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times
    Article Snippet: Cells were lysed using a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) at 6200 rpm for one 45-s pulse. .. The product was purified with 17 μL of Agencourt Ampure XP beads (Beckman Coulter, Brea, CA) and eluted in 21 μL of water.

    Gel Extraction:

    Article Title: Construction of a High-Density Genetic Map and Identification of Loci Related to Hollow Stem Trait in Broccoli (Brassic oleracea L. italica)
    Article Snippet: Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled. .. Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled.

    Cross-linking Immunoprecipitation:

    Article Title: Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus). Population assignment and local adaptation along an isolation‐by‐distance gradient in Pacific cod (Gadus macrocephalus)
    Article Snippet: DNA was extracted from fin clip tissue punches in 96‐well format using a DNeasy 96 Blood & Tissue Kit (Qiagen, Inc., Valencia, CA). .. RAD libraries were prepared, including Sbf I restriction enzyme digestion, adapter ligation, shearing, and PCR amplifications using 500 ng DNA per fish according to Baird et al. ( ) and Hohenlohe, Amish, Catchen, Allendorf, and Luikart , with modification to include Agencourt AMPure XP SPRI beads (Beckman Coulter, Inc., Pasadena, CA) for size selection/exclusion and purification (P.D.

    Biomarker Assay:

    Article Title: Construction of a High-Density Genetic Map and Identification of Loci Related to Hollow Stem Trait in Broccoli (Brassic oleracea L. italica)
    Article Snippet: Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled. .. Next, PCR products were depurated using Agencourt AMPure XP beads (Beckman Coulter, High Wycombe, United Kingdom) and pooled.

    Nanopore Sequencing:

    Article Title: Determining exon connectivity in complex mRNAs by nanopore sequencing
    Article Snippet: Paragraph title: Amplicon library preparation and Oxford Nanopore sequencing ... This reaction mixture was then purified using Agencourt AMPure XP (Beckman Coulter Inc., cat. no. A63880) beads and washed and eluted in nanopore supplied reagents in 25 μL ultrapure water.

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    Beckman Coulter agencourt ampure xp beads
    Drosophila sequencing library. a and b Agarose gel (2%) demonstrating the PCR products from surface tagmentation, various amount of acrydite oligonucleotides were used when casting the poly-acrylamide gel. c Agarose gel (2%) demonstrating the sequencing library after surface tagmentation and 16 cycles of PCR. The sequencing library was size selected with <t>Agencourt</t> <t>Ampure</t> XP beads
    Agencourt Ampure Xp Beads, supplied by Beckman Coulter, used in various techniques. Bioz Stars score: 99/100, based on 1011 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/agencourt ampure xp beads/product/Beckman Coulter
    Average 99 stars, based on 1011 article reviews
    Price from $9.99 to $1999.99
    agencourt ampure xp beads - by Bioz Stars, 2019-10
    99/100 stars
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    99
    Beckman Coulter ampure beads
    cIAP1 is required for the recruitment of E2F1 onto chromatin. ChIP-seq analysis of the recruitment of E2F1 onto chromatin in HeLa cells transfected with scrambled (Sc) or cIAP1-siRNA. Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an ‘A’ base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bio Scientific) using the Bravo Platform (Agilent), size-selected after 4 cycles of <t>PCR</t> with <t>AMPure</t> XP beads (Beckman Coulter) and amplified by PCR for 10 more cycles (A). The efficiency of siRNA was checked by Western Blot analysis (B).
    Ampure Beads, supplied by Beckman Coulter, used in various techniques. Bioz Stars score: 99/100, based on 192 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ampure beads/product/Beckman Coulter
    Average 99 stars, based on 192 article reviews
    Price from $9.99 to $1999.99
    ampure beads - by Bioz Stars, 2019-10
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    Drosophila sequencing library. a and b Agarose gel (2%) demonstrating the PCR products from surface tagmentation, various amount of acrydite oligonucleotides were used when casting the poly-acrylamide gel. c Agarose gel (2%) demonstrating the sequencing library after surface tagmentation and 16 cycles of PCR. The sequencing library was size selected with Agencourt Ampure XP beads

    Journal: BMC Genomics

    Article Title: Next-generation sequencing library construction on a surface

    doi: 10.1186/s12864-018-4797-4

    Figure Lengend Snippet: Drosophila sequencing library. a and b Agarose gel (2%) demonstrating the PCR products from surface tagmentation, various amount of acrydite oligonucleotides were used when casting the poly-acrylamide gel. c Agarose gel (2%) demonstrating the sequencing library after surface tagmentation and 16 cycles of PCR. The sequencing library was size selected with Agencourt Ampure XP beads

    Article Snippet: The PCR products were purified and size selected by Agencourt AMPure XP beads (Beckman Coulter).

    Techniques: Sequencing, Agarose Gel Electrophoresis, Polymerase Chain Reaction, Acrylamide Gel Assay

    cIAP1 is required for the recruitment of E2F1 onto chromatin. ChIP-seq analysis of the recruitment of E2F1 onto chromatin in HeLa cells transfected with scrambled (Sc) or cIAP1-siRNA. Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an ‘A’ base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bio Scientific) using the Bravo Platform (Agilent), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter) and amplified by PCR for 10 more cycles (A). The efficiency of siRNA was checked by Western Blot analysis (B).

    Journal: PLoS ONE

    Article Title: E2F1 binds to the peptide-binding groove within the BIR3 domain of cIAP1 and requires cIAP1 for chromatin binding

    doi: 10.1371/journal.pone.0206253

    Figure Lengend Snippet: cIAP1 is required for the recruitment of E2F1 onto chromatin. ChIP-seq analysis of the recruitment of E2F1 onto chromatin in HeLa cells transfected with scrambled (Sc) or cIAP1-siRNA. Enriched DNA from ChIP and Input DNA fragments were end-repaired, extended with an ‘A’ base on the 3′end, ligated with indexed paired-end adaptors (NEXTflex, Bio Scientific) using the Bravo Platform (Agilent), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter) and amplified by PCR for 10 more cycles (A). The efficiency of siRNA was checked by Western Blot analysis (B).

    Article Snippet: For the ChIP-seq analysis, enriched DNA from ChIP and input DNA fragments were end-repaired, extended with an ‘A’ base on the 3′-end, ligated with indexed paired-end adaptors (NEXTflex, Bio Scientific, Saint-Marcel, France) using the Bravo Platform (Agilent), size-selected after 4 cycles of PCR with AMPure XP beads (Beckman Coulter, Villepinte, France) and amplified by PCR for 10 more cycles.

    Techniques: Chromatin Immunoprecipitation, Transfection, Polymerase Chain Reaction, Amplification, Western Blot