Nextflex poly a beads

Manufactured by PerkinElmer

Sourced in United States

The NEXTflex Poly(A) Beads are a solid-phase magnetic bead-based product designed for the enrichment of polyadenylated RNA from total RNA samples. The beads contain a proprietary poly(A) capture mechanism that selectively binds to the poly(A) tail of mRNA molecules, enabling their isolation and purification.

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Lab products found in correlation

Ambion turbo dna free kit, by Thermo Fisher Scientific (1 mentions) Nextflex rapid directional rna seq kit, by PerkinElmer (1 mentions) Hiseq 2000, by Illumina (1 mentions) Hiseq 2500, by Illumina (1 mentions) Nextseq 500, by Illumina (1 mentions) Truseq stranded total rna library prep kit, by Illumina (1 mentions) Trizol, by Thermo Fisher Scientific (1 mentions) Rneasy plus mini kit, by Qiagen (1 mentions) Nextflex rapid directional rna seq library prep kit, by PerkinElmer (1 mentions) Nextseq 500 instrument, by Illumina (1 mentions) Agilent bioanalyzer, by Agilent Technologies (1 mentions) Nanodrop 2000c spectrophotometer, by Agilent Technologies (1 mentions) R studio v0, by Posit (1 mentions) Nextseq 500 high output flow cell, by Illumina (1 mentions)

Spelling variants of this product

NEXTFLEX® Poly(A) Beads 2.0 (3 citations) NEXTFLEX Poly(A) Beads 2.0 kit (2 citations)

4 protocols using nextflex poly a beads

Transcriptome Analysis of Drosophila Ovaries

Cited 3 times

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For D. simulans strain w501 and DGRP strains 313, 362, 379, 391, and 732, we used 5 to 20 pairs of ovaries from mated females. The ovaries were dissected in 1× PBS and then immediately transferred to 200-μL RNAlater Solution. Total RNA was extracted using 200-μL Trizol and DNase treated using the Ambion TURBO DNA-free Kit (Invitrogen, Carlsbad, California, USA). The mRNA-seq libraries were prepared using Bioo Scientific NEXTflex Poly(A) Beads and NEXTflex Rapid Directional RNA-Seq Kit (PerkinElmer, Austin, Texas, USA). We obtained additional D. simulans ovary expression data from [92 (link)]. We aligned the RNA-seq data to their respective reference genome assembly using hisat2 [115 (link)] and then used htseq-count [129 (link)] to obtain raw read counts for each gene. We only counted reads overlapping CDS features in case the UTR annotations differed between species. We corrected the raw counts for batch effects using ComBat-seq [130 (link)] and used DESeq2 to normalize the batch-corrected counts and test for differential expression. We only considered genes identified as 1-to-1 orthologs between D. melanogaster and D. simulans by FlyBase and excluded orthologs whose CDS length differed by more than 10 bp.

Ellison C.E., Kagda M.S, & Cao W. (2020). Telomeric TART elements target the piRNA machinery in Drosophila. PLoS Biology, 18(12), e3000689.

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RNA Extraction and Library Preparation Protocol

Cited 2 times

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For cell lines, RNA was prepared using TRIzol (Life Technologies) and extracted using RNeasy Plus Mini kit (Qiagen #74134). For tissue, samples were first homogenized at 17000 rpm for 30 seconds with a tissue homogenizer (Polytron, PT10-35GT). Libraries were prepared from 250-500 ng total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s directions (Illumina, San Diego, Ca.) For SK-N-FI MS2-NLS-ATRX-helicase and CHLA-90 REST knockdown experiments, poly-A RNA was isolated using NEXTFLEX® Poly(A) Beads and libraries prepared with the NEXTFLEX® Rapid Directional RNA-Seq Library Prep Kit (PerkinElmer). Single-end or paired-end 75-100 bp sequencing was performed on HiSeq 2000, HiSeq 2500, or NextSeq500 according to the manufacturer’s protocol (Illumina). RNA-seq in Tazemetostat treated cells SK-N-FI, SK-N-MM and CHLA-90 was performed as described (Chung et al., 2016 (link); Fontanals-Cirera et al., 2017 (link)).

Qadeer Z.A., Valle-Garcia D., Hasson D., Sun Z., Cook A., Nguyen C., Soriano A., Ma A., Griffiths L.M., Zeineldin M., Filipescu D., Jubierre L., Chowdhury A., Deevy O., Chen X., Finkelstein D.B., Bahrami A., Stewart E., Federico S., Gallego S., Dekio F., Fowkes M., Meni D., Maris J.M., Weiss W.A., Roberts S.S., Cheung N.K., Jin J., Segura M.F., Dyer M.A, & Bernstein E. (2019). ATRX in-frame fusion neuroblastoma is sensitive to EZH2 inhibition via modulation of neuronal gene signatures. Cancer cell, 36(5), 512-527.e9.

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Transcriptomics of Midgut and Fat Body

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Midguts and fat bodies (associated with the abdominal cuticle) were
dissected in ice-cold PBS. Dissected tissues were placed directly into ice-cold
Trizol (ThermoFisher Scientific #15596026). Five experimental replicates were
obtained per condition, each containing twelve fat bodies or guts. RNA was
extracted by Trizol-chloroform extraction, quantified on a NanoDrop 2000c
spectrophotometer, and integrity was assessed on an Agilent Bioanalyzer. Poly(A)
RNA was pulled down using NextFlex Poly(A) beads (PerkinElmer NOVA-512981). RNA
fragments were given unique molecular identifiers and libraries were prepared
for sequencing using NextFlex Rapid Directional qRNAseq v2 reagents, (barcode
sets C and D, PerkinElmer NOVA-5130-14 and NOVA-5130-15) and 16 cycles of PCR.
Individual and pooled library quality, size and molarity were assessed on an
Agilent Bioanalyzer and quantified with a Qubit spectrophotometer. Libraries
were pooled at equal molarity in NextFlex resuspension buffer. Due to poor RNA
or library yield/quality, three samples were not sequenced. Sequencing was
performed by the UCL Cancer Institute, using an Illumina NextSeq 500 instrument,
with a single-end 75bp sequencing length.

Corrales G.M., Li M., Svermova T., Goncalves A., Voicu D., Dobson A.J., Southall T.D, & Alic N. (2022). Transcriptional memory of dFOXO activation in youth curtails later-life mortality through chromatin remodelling and Xbp1. Nature aging, 2, 1176-1190.

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Transcriptomic Analysis via NextSeq 500

Cited 1 time

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Transcriptomic analysis was performed at ViroScan3D/ProfileXpert platform (www.viroscan3d.com). Briefly, RNA from each sample was quantified using Quantus HSRNA method (Promega) and qualified using Fragment analyzer HSRNA (AATI). After quality control, total RNA were submitted to polyA capture using NextFlex poly(A) Beads (PerkinElmer, Waltham, MA, USA), then mRNA were submitted to library preparation using NextFlex Rapid Directional mRNA (PerkinElmer) and 100 ng input. As recommended by the ENCODE (Encyclopedia of DNA Elements) consortium ERCC (External RNA Control Consortium) RNA spike-In (Invitrogen) were added to samples in order to ensure reproducibility of the experiments. Single-read sequencing with 75 bp read length was performed on NextSeq 500 high output flowcell (Illumina). Mapped reads for each samples were counted and normalized using FPKM method [59 (link)]. Fold change between the different groups were calculated using median of groups and p-value of difference were calculated using t-test with equal variance without p-value correction in the RStudio v.0.99.893 (RStudio Inc., Boston, MA, USA). Heatmaps were performed thanks to Heatmapper [60 (link)], using average linkage clustering method and Pearson distance measurement method.

Genestet C., Hodille E., Barbry A., Berland J.L., Hoffmann J., Westeel E., Bastian F., Guichardant M., Venner S., Lina G., Ginevra C., Ader F., Goutelle S, & Dumitrescu O. (2021). Rifampicin exposure reveals within-host Mycobacterium tuberculosis diversity in patients with delayed culture conversion. PLoS Pathogens, 17(6), e1009643.

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