Rnaclean xp beads

Manufactured by Beckman Coulter

Sourced in United States

RNAClean XP beads are magnetic beads designed for the purification and isolation of RNA from a variety of sample types. They provide a simple and efficient method for the capture, washing, and elution of RNA molecules.

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Lab products found in correlation

Nextseq 500, by Illumina (18 mentions) Nextera xt dna library preparation kit, by Illumina (14 mentions) Ampure xp bead, by Beckman Coulter (14 mentions) Maxima reverse transcriptase, by Thermo Fisher Scientific (10 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (10 mentions) Turbo dnase, by Thermo Fisher Scientific (8 mentions) Kapa hotstart hifi 2 readymix, by Roche (8 mentions) Dnase 1, by New England Biolabs (8 mentions) Truseq stranded total rna library prep kit, by Illumina (7 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (6 mentions) 2100 bioanalyzer, by Agilent Technologies (5 mentions) Superscript 3 reverse transcriptase, by Thermo Fisher Scientific (5 mentions) Tcl buffer, by Qiagen (5 mentions) High sensitivity dna chip, by Agilent Technologies (4 mentions) Nextseq 500 platform, by Illumina (4 mentions) Tapestation, by Agilent Technologies (4 mentions) Nextera kit, by Illumina (3 mentions) T4 dna ligase, by New England Biolabs (3 mentions) Hiseq 2500, by Illumina (3 mentions) Ribo zero gold rrna removal kit, by Illumina (3 mentions)

Close spelling variants of this product

Agencourt RNAClean XP beads (106 citations) RNAClean XP (39 citations) RNAclean beads (10 citations) RNAClean XP magnetic beads (10 citations) Agencourt RNAClean XP magnetic beads (8 citations) AMPure/RNAClean XP beads (6 citations) Agencourt RNAClean XP SPRI beads (5 citations) RNAClean XP Kit magnetic beads (2 citations) RNAClean XP SPRI beads (2 citations) Agencourt AMPure RNAClean XP beads (2 citations)

119 protocols using rnaclean xp beads

SARS-CoV-2 Whole Genome Sequencing and Variant Analysis

Cited 1 time

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Viral RNAs were extracted from nasopharyngeal swabs by using QIAamp Viral RNA Mini Kit, followed by purification with Agencourt RNAClean XP beads. Both the concentration and the quality of all isolated RNA samples were measured and checked with the Nanodrop.
Amplicons of whole genome sequences of SARS-CoV-2 were generated with a 50 ng viral RNA template, by using CleanPlex SARS-CoV-2 Research and Surveillance Panel, QIAseq DIRECT SARSCoV-2 Kit and Illumina COVIDSeq Assay following manufacters’ protocol. Libraries were then generated using the Nextera DNA Flex library preparation kit with Illumina index adaptors and sequenced on a MiSeq instrument (Illumina, San Diego, CA, USA) with 2 × 150-bp paired-end reads. Raw reads were trimmed for adapters and filtered for quality (Phred score > 28) using Fastp (v0.23.2)^{52 (link)}. Reference-based assembly was performed with BWA-mem (v0.7.17)^{53 (link)} aligning against the GenBank reference genome NC_045512.2 (Wuhan, collection date: December 2019).
SNP variants were called with freebayes (v1.3.2)⁵⁴ and all SNPs having a minimum supporting read frequency of 2% with a depth ≥ 10 were retained.
Synonymous and non-synonymous SNPs characterizing Omicron lineages were defined as high-abundant mutations if characterized by a read frequency ≥ 40%, and low-abundant mutations if characterized by a read frequency between 2 and 40%.

Scutari R., Fox V., Fini V., Granaglia A., Vittucci A.C., Smarrazzo A., Lancella L., Calo’ Carducci F., Romani L., Cursi L., Bernaschi P., Russo C., Campana A., Bernardi S., Villani A., Perno C.F, & Alteri C. (2024). Molecular characterization of SARS-CoV-2 Omicron clade and clinical presentation in children. Scientific Reports, 14, 5325.

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Single-cell RNA-sequencing of mouse endothelial cells

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For each mouse, 1,000 PP FRCs or HEV ECs were sorted into 5 μl/well of TCL (Qiagen #1031576) buffer containing 1% 2-mercaptoethanol. RNA was isolated using RNAClean XP beads (Agencourt A63987). Template switching, cDNA synthesis and cDNA amplification were adapted from previous studies^{38 (link)}. Libraries were prepared using the Nextera kit (Illumina). Libraries were sequenced using an Illumina HiSeq yielding, on average, 27.5 million reads pairs per sample. RNA-sequencing data were analyzed using HTSeqGenie package in BioConductor^{39 (link)} as follows: first, reads with low nucleotide qualities (70% of bases with quality <23) or rRNA and adapter contamination were removed. The reads that passed were then aligned to the reference genome GRCh37 using GSNAP^{40 (link)}. 1.6 – 4.3 % reads were of low quality and were removed. The percentage rRNA contamination ranged from 1.16 – 4.64 %. These were also removed. Reads that were uniquely mapped were used for subsequent analysis. Gene expression levels were quantified as Reads Per Kilobase of exon model per Million mapped reads normalized by size factor (nRPKM), defined as number of reads aligning to a gene in a sample / (total number of uniquely mapped reads for that sample × gene length × size factor). Differential expression analysis was performed using voom/limma^{41 (link)}.

Chang J.E., Buechler M.B., Gressier E., Turley S.J, & Carroll M.C. (2019). Mechanosensing by Peyer’s patch stroma regulates lymphocyte migration and mucosal antibody responses. Nature immunology, 20(11), 1506-1516.

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cDNA Library Generation from RNA

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To generate cDNA libraries, 1,000 pg total RNA were amplified and converted to cDNA using NuGEN's Ovation RNA-Seq kit V2. In brief, the mRNA was reverse transcribed to synthesize the first-strand cDNA by using a combination of random hexamers and a poly-T chimeric primer. Double-stranded DNA is generated by fragmentation of the mRNA template strand using RNA-dependent DNA polymerase. The double-stranded DNA was purified using Agencourt RNAClean XP beads. The DNA is amplified linearly using a SPIA process in which RNase H degrades RNA in DNA/RNA heteroduplex at the 5′-end of the double-stranded cDNA, after which the SPIA primer binds to the cDNA and the polymerase starts replication at the 3′-end of the primer by displacement of the existing forward strand. Finally, random hexamers were used to amplify the second-strand cDNA linearly. Following amplification, 5.0 μg cDNA was fragmented to ∼200 bp using the Covaris S2 and the fragmentation parameters described in the Encore SP Rapid DR Multiplex library preparation protocol (NuGEN). The remainder of the library preparation followed the manufacturer's protocol as described in Encore SP Rapid DR Multiplex System. Paired-end sequencing of bar-coded cDNA libraries at 101 cycles (100 bases each end) was carried out on a HiSeq 1000. The raw sequence data have been deposited to GEO with accession number GSE63147.

Böttcher J.P., Beyer M., Meissner F., Abdullah Z., Sander J., Höchst B., Eickhoff S., Rieckmann J.C., Russo C., Bauer T., Flecken T., Giesen D., Engel D., Jung S., Busch D.H., Protzer U., Thimme R., Mann M., Kurts C., Schultze J.L., Kastenmüller W, & Knolle P.A. (2015). Functional classification of memory CD8+ T cells by CX3CR1 expression. Nature Communications, 6, 8306.

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Viral RNA Isolation and Sequencing

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RNA was extracted from serum and cell culture supernatant samples using the ZR-96 Viral DNA/RNA Kit from Zymo Research (Irvine, CA, USA). Samples were then DNase treated with TURBO DNase (ThermoFisher) and purified using RNAClean XP beads (Agencourt). Library preparation for NGS was performed using the Trio RNA-Seq kit (NuGEN), which creates, amplifies, and fragments cDNA and then depletes ribosomal RNA. We then sequenced the libraries on an Illumina NextSeq500 using single-end 150bp reads.

Weger-Lucarelli J., Carrau L., Levi L.I., Rezelj V., Vallet T., Blanc H., Boussier J., Megrian D., Coutermarsh-Ott S., LeRoith T, & Vignuzzi M. (2019). Host nutritional status affects alphavirus virulence, transmission, and evolution. PLoS Pathogens, 15(11), e1008089.

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Single-Cell RNA-Seq Library Preparation

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Libraries were prepared using a modified SMART-Seq2 protocol as previously reported (Picelli et al., 2014). Briefly, RNA lysate cleanup was performed using RNAClean XP beads (Agencourt), followed by reverse transcription with Maxima Reverse Transcriptase (Life Technologies) and whole transcription amplification (WTA) with KAPA HotStart HIFI 2× ReadyMix (Kapa Biosystems) for 21 cycles. WTA products were purified with Ampure XP beads (Beckman Coulter), quantified with Qubit dsDNA HS Assay Kit (ThermoFisher), and assessed with a high sensitivity DNA chip (Agilent). RNA-seq libraries were constructed from purified WTA products using Nextera XT DNA Library Preparation Kit (Illumina). On each plate, the population and no-cell controls were processed using the same method as the single cells. The libraries were sequenced on an Illumina NextSeq 500.

Beyaz S., Chung C., Mou H., Bauer-Rowe K.E., Xifaras M.E., Ergin I., Dohnalova L., Biton M., Shekhar K., Eskiocak O., Papciak K., Ozler K., Almeqdadi M., Yueh B., Fein M., Annamalai D., Valle-Encinas E., Erdemir A., Dogum K., Shah V., Alici-Garipcan A., Meyer H.V., Özata D.M., Elinav E., Kucukural A., Kumar P., McAleer J.P., Fox J.G., Thaiss C.A., Regev A., Roper J., Orkin S.H, & Yilmaz Ö.H. (2021). Dietary suppression of MHC-II expression in intestinal epithelial cells enhances intestinal tumorigenesis. Cell stem cell, 28(11), 1922-1935.e5.

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SARS-CoV-2 Genome Sequencing Protocol

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Viral RNAs were extracted from nasopharyngeal swabs by using QIAamp Viral RNA Mini Kit, followed by purification with Agencourt RNAClean XP beads. Both the concentration and the quality of all isolated RNA samples were measured and checked with the Nanodrop. Amplicons of whole genome sequences of SARS-CoV-2 were generated with a 50 ng viral RNA template, by using a multiplex approach e.g. CleanPlex SARS-CoV-2 Research and Surveillance Panel, and QIAseq DIRECT SARS-CoV-2 Kit^{18 ,19} according to the manufacturer’s protocol. Libraries were then generated using the Nextera DNA Flex library preparation kit with Illumina index adaptors and sequenced on a MiSeq instrument (Illumina, San Diego, CA, USA) with 2 × 150-bp paired-end reads.
Reference-based assembly of the raw data was performed according to^{20 (link)}. 612 consensus sequences were generated using the GitHub freely distributed software vcf_consensus_builder²¹. All SNPs having a minimum supporting read frequency of 40% with a depth ≥ 10 were retained.

Alteri C., Scutari R., Costabile V., Colagrossi L., Yu La Rosa K., Agolini E., Lanari V., Chiurchiù S., Romani L., Markowich A.H., Bernaschi P., Russo C., Novelli A., Bernardi S., Campana A., Villani A, & Perno C.F. (2022). Epidemiological characterization of SARS-CoV-2 variants in children over the four COVID-19 waves and correlation with clinical presentation. Scientific Reports, 12, 10194.

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RNA-Seq Library Preparation and Sequencing

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RNA concentration and quality were determined with Agilent 2100 Bioanalyzer using an Agilent RNA 6000 Nano Kit. RNA samples were purified with Agencourt RNAClean XP beads prior to library preparation. Illumina TruSeq Stranded Total RNA LT kit was used to deplete ribosomal RNA (rRNA) and construct cDNA libraries according to the instructions provided by the manufacturer. RNA was fragmented, converted to double-stranded cDNA, and adapters ligated to each strand. The resulting ~300 base-pair cDNA fragments were then amplified by PCR and purified using AMPureXP Beads. Each library was prepared with a unique indexed adapter for multiplexing. Libraries were validated for size, concentration, and integrity with Agilent 2100 Bioanalyzer using Agilent High Sensitivity DNA Kit. Multiplexed libraries were subjected to single-end 75 base pair sequencing using the Illumina NextSeq500 V2 platform.

Woolsey C., Jankeel A., Matassov D., Geisbert J.B., Agans K.N., Borisevich V., Cross R.W., Deer D.J., Fenton K.A., Latham T.E., Gerardi C.S., Mire C.E., Eldridge J.H., Messaoudi I, & Geisbert T.W. (2020). Immune correlates of postexposure vaccine protection against Marburg virus. Scientific Reports, 10, 3071.

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rRNA-depleted RNA-seq library generation

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To generate rRNA-depleted RNA-seq libraries, 2.5-5 μg of total RNA from sorted cells was reverse-transcribed using a mix of biotinylated antisense oligos [73 (link)] with PrimeScript Reverse transcriptase (Takara). The resulting RNA:DNA hybrid was subjected to pull-down using two aliquots of 100 μL strepatavidin magnetic beads (Dynabeads MyOne Streptavidin C1, Invitrogen). rRNA depleted RNA was purified with Agencourt RNAclean XP beads. Reverse transcription and streptavidin pull-down with two 100 μL aliquots of magnetic beads was repeated for the second time. Double rRNA depleted RNA was purified with Agencourt RNA clean XP beads and stored at −80⁰C. For nuclear RNA samples the same procedure was applied, except that only a single rRNA removal was performed on the total RNA obtained (typically ∼1 μg). Ribodepletion was assessed both by Bioanalyzer analysis and by qPCR.

Schor I.E., Bussotti G., Maleš M., Forneris M., Viales R.R., Enright A.J, & Furlong E.E. (2018). Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis. Current Biology, 28(22), 3547-3561.e9.

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Single-cell RNA-seq library preparation

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Single cells were processed using a modified SMART-Seq2 protocol as previously described^{44 (link)}. Briefly, RNAClean XP beads (Agencourt) were used for RNA lysate cleanup, followed by reverse transcription using Maxima Reverse Transcriptase (Life Technologies), whole transcription amplification (WTA) with KAPA HotStart HIFI 2X ReadyMix (Kapa Biosystems) for 21 cycles and purification using AMPure XP beads (Agencourt). WTA products were quantified with Qubit dsDNA HS Assay Kit (ThermoFisher), visualized with high sensitivity DNA Analysis Kit (Agilent) and libraries were constructed using Nextera XT DNA Library Preparation Kit (Illumina). Population and no-cell controls were processed with the same methods as singe cells. Libraries were sequenced on an Illumina NextSeq 500.

Montoro D.T., Haber A.L., Biton M., Vinarsky V., Lin B., Birket S., Yuan F., Chen S., Leung H.M., Villoria J., Rogel N., Burgin G., Tsankov A., Waghray A., Slyper M., Waldmann J., Nguyen L., Dionne D., Rozenblatt-Rosen O., Tata P.R., Mou H., Shivaraju M., Bihler H., Mense M., Tearney G.J., Rowe S.M., Engelhardt J.F., Regev A, & Rajagopal J. (2018). A revised airway epithelial hierarchy includes CFTR-expressing ionocytes. Nature, 560(7718), 319-324.

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Single-Cell RNA-seq Library Preparation

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Libraries were prepared using a modified SMART-Seq2 protocol as previously reported^{16 (link)}. Briefly, RNA lysate cleanup was preformed using RNAClean XP beads (Agencourt) followed by reverse transcription with Maxima Reverse Transcriptase (Life Technologies) and whole transcription amplification (WTA) with KAPA HotStart HIFI 2× ReadyMix (Kapa Biosystems) for 21 cycles. WTA products were purified with Ampure XP beads (Beckman Coulter), quantified with Qubit dsDNA HS Assay Kit (ThermoFisher), and assessed with a high sensitivity DNA chip (Agilent). RNA-seq libraries were constructed from purified WTA products using Nextera XT DNA Library Preperation Kit (Illumina). On each plate, the population and no-cell controls were processed using the same method as the single cells. The libraries were sequenced on an Illumina NextSeq 500.

Haber A.L., Biton M., Rogel N., Herbst R.H., Shekhar K., Smillie C., Burgin G., Delorey T.M., Howitt M.R., Katz Y., Tirosh I., Beyaz S., Dionne D., Zhang M., Raychowdhury R., Garrett W.S., Rozenblatt-Rosen O., Shi H.N., Yilmaz O., Xavier R.J, & Regev A. (2017). A single-cell survey of the small intestinal epithelium. Nature, 551(7680), 333-339.

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