ampure xp beads system  (Beckman Coulter)


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    Structured Review

    Beckman Coulter ampure xp beads system
    Ampure Xp Beads System, supplied by Beckman Coulter, used in various techniques. Bioz Stars score: 88/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ampure xp beads system/product/Beckman Coulter
    Average 88 stars, based on 10 article reviews
    Price from $9.99 to $1999.99
    ampure xp beads system - by Bioz Stars, 2020-07
    88/100 stars

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    Related Articles

    Polymerase Chain Reaction:

    Article Title: Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.)
    Article Snippet: .. Double-stranded cDNAs were synthesized using random hexamers and M-MuLV Reverse Transcriptase (RNase H-), followed by DNA Polymerase I and RNase H. After adenylation of the 3′ ends of cDNA fragments, NEBNext adapter oligonucleotides were ligated to cDNA fragments, and the AMPure XP beads system (Beckman Coulter, Beverly, USA) was used to select cDNA fragments of approximately 200 bp in length. cDNA fragments with ligated adapter molecules on both ends were selectively enriched using the NEB Universal PCR Primer and Index primer in a 10-cycle PCR reaction. .. Products were purified with the AMPure XP beads system and quantified using the Agilent Bioanalyzer 2100 system.

    Article Title: Clock-dependent chromatin topology modulates circadian transcription and behavior
    Article Snippet: .. PCR products were purified with the AMPure XP beads system (Beckman Coulter), and amplification profiles were analyzed by fragment analyzer and then sequenced on Illumina HiSeq 2000 machines using single-end 100-bp read length. .. Six-hundred nanograms of 4C template was used for PCR amplification using Sigma-Aldrich long-template PCR system with two-step PCR system from Illumina.

    Article Title: Clock-dependent chromatin topology modulates circadian transcription and behavior
    Article Snippet: .. PCR products were purified with the AMPure XP beads system (Beckman Coulter) and then sequenced on NextSeq 500 machines using single-end 75-bp read length. ..

    cDNA Library Assay:

    Article Title: Exploring the Genetic Basis of Adaptation to High Elevations in Reptiles: A Comparative Transcriptome Analysis of Two Toad-Headed Agamas (Genus Phrynocephalus)
    Article Snippet: .. Random oligonucleotides and M-MuLV Reverse Transcriptase (RNase H-) were used to synthesize the first cDNA strand, and the second cDNA strand was synthesized using DNA Polymerase I and RNase H. The cDNA library with an insert size of ∼200 base pairs (bps) was targeted and purified with AMPure XP beads system (Beckman Coulter ), and subsequently sequenced on an Illumina HiSeq 2000 platform. ..

    Amplification:

    Article Title: Clock-dependent chromatin topology modulates circadian transcription and behavior
    Article Snippet: .. PCR products were purified with the AMPure XP beads system (Beckman Coulter), and amplification profiles were analyzed by fragment analyzer and then sequenced on Illumina HiSeq 2000 machines using single-end 100-bp read length. .. Six-hundred nanograms of 4C template was used for PCR amplification using Sigma-Aldrich long-template PCR system with two-step PCR system from Illumina.

    Synthesized:

    Article Title: Transcriptomic analysis reveals the roles of microtubule-related genes and transcription factors in fruit length regulation in cucumber (Cucumis sativus L.)
    Article Snippet: .. Double-stranded cDNAs were synthesized using random hexamers and M-MuLV Reverse Transcriptase (RNase H-), followed by DNA Polymerase I and RNase H. After adenylation of the 3′ ends of cDNA fragments, NEBNext adapter oligonucleotides were ligated to cDNA fragments, and the AMPure XP beads system (Beckman Coulter, Beverly, USA) was used to select cDNA fragments of approximately 200 bp in length. cDNA fragments with ligated adapter molecules on both ends were selectively enriched using the NEB Universal PCR Primer and Index primer in a 10-cycle PCR reaction. .. Products were purified with the AMPure XP beads system and quantified using the Agilent Bioanalyzer 2100 system.

    Article Title: The draft genome assembly of Rhododendron delavayi Franch. var. delavayi
    Article Snippet: .. Random oligo-nucleotides and M-MuLV Reverse Transcriptase (RNase H) were used to synthesize the first cDNA strand, and then the second cDNA strand was synthesized using DNA Polymerase I and RNase H. The cDNA libraries with insert sizes of 200–500 base pairs (bps) were selected and purified with the AMPure XP beads system (Beckman Coulter), and subsequently sequenced on an Illumina HiSeq 2000 platform. .. Both cDNA library construction and Illumina sequencing were carried out by BGI-ShenZhen.

    Article Title: Exploring the Genetic Basis of Adaptation to High Elevations in Reptiles: A Comparative Transcriptome Analysis of Two Toad-Headed Agamas (Genus Phrynocephalus)
    Article Snippet: .. Random oligonucleotides and M-MuLV Reverse Transcriptase (RNase H-) were used to synthesize the first cDNA strand, and the second cDNA strand was synthesized using DNA Polymerase I and RNase H. The cDNA library with an insert size of ∼200 base pairs (bps) was targeted and purified with AMPure XP beads system (Beckman Coulter ), and subsequently sequenced on an Illumina HiSeq 2000 platform. ..

    Purification:

    Article Title: The draft genome assembly of Rhododendron delavayi Franch. var. delavayi
    Article Snippet: .. Random oligo-nucleotides and M-MuLV Reverse Transcriptase (RNase H) were used to synthesize the first cDNA strand, and then the second cDNA strand was synthesized using DNA Polymerase I and RNase H. The cDNA libraries with insert sizes of 200–500 base pairs (bps) were selected and purified with the AMPure XP beads system (Beckman Coulter), and subsequently sequenced on an Illumina HiSeq 2000 platform. .. Both cDNA library construction and Illumina sequencing were carried out by BGI-ShenZhen.

    Article Title: Transcriptome Profile of the Green Odorous Frog (Odorrana margaretae)
    Article Snippet: .. The second cDNA strand synthesis was subsequently performed using DNA Polymerase I and RNase H. The cDNA with an insert size of 200 bp were preferentially purified with AMPure XP beads system (Beckman Coulter) and sequenced on an Illumina HiSeq 2000 platform. .. 101 bp paired-end reads were generated and all raw sequence read data were stored in FastQ format.

    Article Title: Clock-dependent chromatin topology modulates circadian transcription and behavior
    Article Snippet: .. PCR products were purified with the AMPure XP beads system (Beckman Coulter), and amplification profiles were analyzed by fragment analyzer and then sequenced on Illumina HiSeq 2000 machines using single-end 100-bp read length. .. Six-hundred nanograms of 4C template was used for PCR amplification using Sigma-Aldrich long-template PCR system with two-step PCR system from Illumina.

    Article Title: Clock-dependent chromatin topology modulates circadian transcription and behavior
    Article Snippet: .. PCR products were purified with the AMPure XP beads system (Beckman Coulter) and then sequenced on NextSeq 500 machines using single-end 75-bp read length. ..

    Article Title: Exploring the Genetic Basis of Adaptation to High Elevations in Reptiles: A Comparative Transcriptome Analysis of Two Toad-Headed Agamas (Genus Phrynocephalus)
    Article Snippet: .. Random oligonucleotides and M-MuLV Reverse Transcriptase (RNase H-) were used to synthesize the first cDNA strand, and the second cDNA strand was synthesized using DNA Polymerase I and RNase H. The cDNA library with an insert size of ∼200 base pairs (bps) was targeted and purified with AMPure XP beads system (Beckman Coulter ), and subsequently sequenced on an Illumina HiSeq 2000 platform. ..

    Article Title: Transcriptomic Profiles Reveal the Interactions of Cd/Zn in Dwarf Polish Wheat (Triticum polonicum L.) Roots
    Article Snippet: .. Then, 200-bp cDNA fragments were purified using the AMPure XP beads system (Beckman Coulter, USA). .. Ten cycles of PCR amplifications were performed to enrich cDNA fragments using the NEB Universal PCR primer and Index primer (Illumia, USA).

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  • 94
    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).
    Ampure Xp Beads, supplied by Beckman Coulter, used in various techniques. Bioz Stars score: 94/100, based on 2560 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/ampure xp beads/product/Beckman Coulter
    Average 94 stars, based on 2560 article reviews
    Price from $9.99 to $1999.99
    ampure xp beads - by Bioz Stars, 2020-07
    94/100 stars
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    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

    Work flow of the standard versus DDAT library preparation method. To generate WGS libraries from low-input, degraded DNA, the complete protocol starts with the addition of enzymes SMUG1 (single-strand-selective monofunctional uracil-DNA glycosylase) and Fpg (formamidopyrimidine [fapy]-DNA glycosylase) to the input DNA ( A and B ) that remove damaged bases such as deoxyuracil and 8-oxoguanine, caused by the FFPE treatment. A short denaturation step (B) is followed by the first strand synthesis; during this step, the genomic DNA, primers and Klenow fragment (3′ → 5′ exo-) are gradually heated from 4 to 37°C with a slow ramping speed of 4°C/min, which is an essential reaction condition (see ‘Discussion’ section), before incubation at 37°C for a further 1.5 h ( C ). The primers contain nine random nucleotides from the 3′-end, in addition to the standard Illumina adaptor sequence, and will anneal to complementary DNA sequences present in the DNA sample. After the first strand synthesis, any remaining primers or short ssDNA fragments are digested with exonuclease I and the dsDNA is purified with AMPure XP beads. Next, the dsDNA is denatured to carry out the second strand synthesis using a second adaptor primer also containing nine random nucleotides, with the same conditions as the first synthesis, followed by bead purification (C). Finally, 10 PCR cycles are carried out using standard Illumina p5 and p7 indexed primers ( D ). The library is purified and assessed using standard quality control methods.

    Journal: Nar Genomics and Bioinformatics

    Article Title: A novel use of random priming-based single-strand library preparation for whole genome sequencing of formalin-fixed paraffin-embedded tissue samples

    doi: 10.1093/nargab/lqz017

    Figure Lengend Snippet: Work flow of the standard versus DDAT library preparation method. To generate WGS libraries from low-input, degraded DNA, the complete protocol starts with the addition of enzymes SMUG1 (single-strand-selective monofunctional uracil-DNA glycosylase) and Fpg (formamidopyrimidine [fapy]-DNA glycosylase) to the input DNA ( A and B ) that remove damaged bases such as deoxyuracil and 8-oxoguanine, caused by the FFPE treatment. A short denaturation step (B) is followed by the first strand synthesis; during this step, the genomic DNA, primers and Klenow fragment (3′ → 5′ exo-) are gradually heated from 4 to 37°C with a slow ramping speed of 4°C/min, which is an essential reaction condition (see ‘Discussion’ section), before incubation at 37°C for a further 1.5 h ( C ). The primers contain nine random nucleotides from the 3′-end, in addition to the standard Illumina adaptor sequence, and will anneal to complementary DNA sequences present in the DNA sample. After the first strand synthesis, any remaining primers or short ssDNA fragments are digested with exonuclease I and the dsDNA is purified with AMPure XP beads. Next, the dsDNA is denatured to carry out the second strand synthesis using a second adaptor primer also containing nine random nucleotides, with the same conditions as the first synthesis, followed by bead purification (C). Finally, 10 PCR cycles are carried out using standard Illumina p5 and p7 indexed primers ( D ). The library is purified and assessed using standard quality control methods.

    Article Snippet: The remaining primers were digested with 20 U of exonuclease I (NEB) at 37°C for 1 h in 100 μl before purification using AMPure XP beads (Beckman).

    Techniques: Formalin-fixed Paraffin-Embedded, Incubation, Sequencing, Purification, Polymerase Chain Reaction

    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

    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