Kapa hyperpure beads

Manufactured by Roche

Sourced in Switzerland

KAPA HyperPure Beads are magnetic, paramagnetic beads designed for use in nucleic acid purification and size selection applications. The beads are composed of a proprietary material and coated with a hydrophilic polymer. They provide efficient and consistent binding and recovery of DNA and RNA molecules across a range of fragment sizes.

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Lab products found in correlation

Ligation sequencing kit, by Oxford Nanopore (1 mentions) R9 flow cell, by Oxford Nanopore (1 mentions) Dneasy blood and tissue kit, by Qiagen (1 mentions) Flow cell wash kit, by Oxford Nanopore (1 mentions) Novaseq 6000 platform, by Illumina (1 mentions) Kapa hyperplus kit, by Roche (1 mentions) Ampure xp bead, by Beckman Coulter (1 mentions) Dneasy powersoil dna extraction kit, by Qiagen (1 mentions) Kapa hifi hotstart readymix, by Roche (1 mentions) Qubit dsdna hs analysis kit, by Thermo Fisher Scientific (1 mentions) Blood genomic dna extraction kit, by Tiangen Biotech (1 mentions) Qubit 4.0 fluorometer, by Thermo Fisher Scientific (1 mentions) Novaseq 6000, by Illumina (1 mentions) Qiaamp dna ffpe tissue kit, by Qiagen (1 mentions) T4 dna ligase, by Tiangen Biotech (1 mentions) Kapa hyper exome, by Roche (1 mentions) Kapa library amplification primer mix, by Roche (1 mentions) Nanodrop, by Thermo Fisher Scientific (1 mentions) Qiamp dna mini kit, by Qiagen (1 mentions)

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Kapa beads (4 citations)

5 protocols using kapa hyperpure beads

Long-read gDNA Sequencing Protocol

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Extraction of genomic DNA from cells was done using the DNeasy Blood and Tissue kit from Qiagen according to the manufacture's instructions. Extracted gDNA was quantified using the Nanodrop reader and gel electrophoresis.
gDNA was fragmented by sonication with a Bioruptor sonicator for 30 cycles of 5 s ON–90 s OFF, using low intensity settings. gDNA was then purified with the Zymo DNA Clean & Concentrator™-5 columns (Zymo Research, D4013) and size selected with 0.4 × volume of KAPA HyperPure Beads (Roche, 08963835001) to exclude small DNA fragments. 1 μg of sheared gDNA was used for library preparation using Ligation Sequencing Kits (Oxford Nanopore Technologies, LSK109 and LSK110) according to the manufacturer’s specifications. Samples were sequenced on a MinION sequencer on R9 Flow Cells (Oxford Nanopore Technologies FLO-MIN106D), using the MinKNOW software v19. Flowcells were washed and reloaded with the Flow Cell Wash Kit (Oxford Nanopore Technologies EXP-WSH003) to increase sequencing depth obtained per flowcell. Average read N50 for sequencing runs was 3 kb.

Khelifi G., Chow T., Whiteley J., Fort V., Humphreys B.D., Hussein S.M, & Rogers I.M. (2022). Determining epigenetic memory in kidney proximal tubule cell derived induced pluripotent stem cells using a quadruple transgenic reprogrammable mouse. Scientific Reports, 12, 20340.

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Halite Metagenome Extraction and Sequencing

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Total DNA was extracted from 2 to 5 g of grounded halite using the DNeasy Powersoil DNA extraction kit (QIAGEN). The DNA was cleaned with 3× AMPure XP Beads (Beckman Coulter) before library construction. The KAPA HyperPlus kit (Roche) was used to construct the genomic libraries with 10 ng of DNA, following the manufacturer’s instructions and with the DNA from each nodule barcoded separately. Final library size selection was made with 0.5× and 0.7× KAPA HyperPure beads (Roche) ratio to recover fragments 300–500 bp in length. Five libraries for Salar Grande and 3 for the other locations were paired-end sequenced by Novogene (https://en.novogene.com/) with 150 bp reads length using the Illumina NovaSeq 6000 platform.

Perez-Fernandez C.A., Wilburn P., Davila A, & DiRuggiero J. (2022). Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert. Scientific Reports, 12, 20022.

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Comprehensive DNA Extraction and Sequencing

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For FFPE samples, genomic DNA was extracted from ten tumor sections of 5 μm using QIAamp DNA FFPE Tissue Kit (Qiagen GmbH). For blood samples, DNA was extracted from peripheral blood lymphocytes (PBL) using a blood genomic DNA Extraction Kit (centrifugal column method) (Tiangen Biotech (Beijing) Co., Ltd). For fresh tumor tissues, DNA was extracted using MagPure FFPE DNA LQ Kit F (Magen Biotechnology Co., Ltd). DNA was quantified using the Qubit 4.0 fluorometer and Qubit dsDNA HS Analysis Kit (Thermo Fisher Scientific, Inc.) according to the manufacturer's instructions. 5× WGS fragmentation mix, 10× WGS fragmentation buffer, T4 DNA Ligase, 5× rapid ligation buffer (Tiangen Biotech (Beijing) Co., Ltd.), KAPA HiFi HotStart Readymix, KAPA Library Amplification Primer Mix (Roche molecular systems, Inc.) were used for library construction. Then, the library was purified by KAPA HyperPure Beads (Roche molecular systems, Inc.). Hybridization capture was carried out using the combined probe of KAPA HyperExplore Max and KAPA HyperExome (Roche molecular systems, Inc.). PCR amplification was carried out for seven to eight cycles according to the input amount of the hybridization library. DNA sequencing was performed on Illumina Novaseq 6000 (Illumina, Inc.) system with an average depth of 650×.

Li Y., Guo Y., Cheng Z., Tian C., Chen Y., Chen R., Yu F., Shi Y., Su F., Zhao S., Wang Z., Luo J, & Tan H. (2023). Whole-exome sequencing of rectal neuroendocrine tumors. Endocrine-Related Cancer, 30(9), e220257.

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Magnetic Bead-Based DNA Cleanup Protocol

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Magnetic beads were sometimes used to clean the extracted DNA products. We used KAPA HyperPure Beads (Roche, Basel, Switzerland) and Select‐a‐Size DNA MagBead (Zymo Research, Irvine, California, USA) to clean two HMW DNA samples extracted from D. blotianum (Table 1). The volume ratio of beads to sample and the cleanup procedures followed the manufacturer's protocols. The post‐cleanup A₂₆₀/A₂₃₀ and A₂₆₀/A₂₈₀ values indicated that the beads improved the purity of the DNA extractions (e.g., A₂₆₀/A₂₃₀ increased from 1.26 to 2.26; Table 1). Some established protocols also use magnetic beads to purify and concentrate HMW DNAs (Mayjonade et al., 2016 (link); Russo et al., 2022 (link)). The cleaned extractions retained DNA fragments of acceptable length for long‐read sequencing (D. blotianum in Table 1), although we did not compare the DNA sizes before and after the cleanup. In the case of the Nephrolepis biserrata (Sw.) Schott gametophyte, a high‐concentration salt solution (1/10 volume of 3 M NaOAc) was added to the cool isopropanol to reduce the precipitation of polysaccharides (Nishii et al., 2022 (link)). With this high‐salt treatment, the A₂₆₀/A₂₃₀ of the resultant DNA extraction was improved to 1.49, while the A₂₆₀/A₂₃₀ ranged from 0.29 to 1.11 in samples without any treatment.

Xie P., Ke Y, & Kuo L. (2023). Modified CTAB protocols for high‐molecular‐weight DNA extractions from ferns. Applications in Plant Sciences, 11(3), e11526.

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ASF Virus Pol19_53050_C1959/19 Isolation

Cited 1 time

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The ASF virus Pol19_53050_C1959/19 was obtained on the 5th day of the 3rd passage in PPAM cell culture. Then, 2 × 200 µL of the cell culture was subjected to DNA extraction with a QiAMP DNA Mini Kit (Qiagen, Hilden, Germany). Final elution of DNA from the column was performed in triplicate (3 × 30 µL). Obtained DNA (2 × 90 µL) was pooled and cleaned-up using KAPA Hyper Pure Beads (Roche, Basel, Switzerland), and recovered in 20 µL of DNAse/RNAse free water. The final concentration of total DNA was measured with Nanodrop (Thermo Fisher Scientific, Waltham, MA, USA) (15.5 ng/µL), A260/A280 factor reached 1.86. The dsDNA concentration was measured using a Qbit dsDNA High Sensitivity kit (Thermo Fisher Scientific, Waltham, MA, USA) and reached 8.52 ng/µL. The remaining three isolates were prepared as described earlier [2 (link)].

Mazur-Panasiuk N., Walczak M., Juszkiewicz M, & Woźniakowski G. (2020). The Spillover of African Swine Fever in Western Poland Revealed Its Estimated Origin on the Basis of O174L, K145R, MGF 505-5R and IGR I73R/I329L Genomic Sequences. Viruses, 12(10), 1094.

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