Kingfisher cell and tissue dna kit

Manufactured by Thermo Fisher Scientific

Sourced in United States

The KingFisher Cell and Tissue DNA Kit is a product designed for the automated extraction and purification of DNA from a variety of cell and tissue samples. The kit utilizes magnetic bead technology to efficiently capture and isolate DNA, allowing for reliable and consistent results.

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Lab products found in correlation

Maxima first strand cdna synthesis kit, by Thermo Fisher Scientific (2 mentions) Hiseq x, by Illumina (2 mentions) Kingfisher flex magnetic particle processor, by Thermo Fisher Scientific (1 mentions) Miseq reagent kits v3, by Illumina (1 mentions) Nextera xt library construction protocol and index kit, by Illumina (1 mentions) Miseq sequencer, by Illumina (1 mentions) Nextseq 500 sequencing system, by Illumina (1 mentions) Nextera xt dna library prep kit, by Illumina (1 mentions) Kingfisher duo prime magnetic particle processor, by Thermo Fisher Scientific (1 mentions) Hiseq x lane, by Illumina (1 mentions) Kingfisher flex system, by Thermo Fisher Scientific (1 mentions) Sybr green qpcr master mix, by Takara Bio (1 mentions) Rneasy micro kit, by Qiagen (1 mentions) Genomic tip, by Qiagen (1 mentions) Magattract hmw dna kit, by Thermo Fisher Scientific (1 mentions) Magmax mirvana total rna isolation kit, by Thermo Fisher Scientific (1 mentions) Rneasy ffpe kit, by Qiagen (1 mentions) Generead dna ffpe kit, by Qiagen (1 mentions) Truseq dna library preparation kit, by Illumina (1 mentions) Kingfisher duo, by Thermo Fisher Scientific (1 mentions)

10 protocols using kingfisher cell and tissue dna kit

Genetic Structure of Introduced and Established Fish Populations

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We studied four groups of fish, that is, released fish representing each of the two distinct populations (introduced population A and introduced population B), and fish established in the wild in lakes Lilla Bävervattnet (established population LB) and Haravattnet (established population HV; Figure 1). The sample size was 50 for each group. Fish from introduced populations A and B were caught in the wild in 1988–1995 and classified to either introduced population based on their age (otolith readings) or by genotype at the allozyme marker locus (Appendix S1; Palm & Ryman, 1999 (link)). Individuals representing the parental generation (P) or the F1 generation for which population assignment was possible using the allozyme marker (no hybrids) are included. Fish established in Lakes LB and HV were caught in 2011.
Genomic DNA was extracted from muscle tissue from 50 individuals from each investigated group (introduced population A, introduced population B, established population LB, and established population HV) using a KingFisher cell and tissue DNA kit (Thermo Scientific) including RNase A treatment. High‐molecular‐weight DNA from each individual was combined at equal concentrations for each population in order to create pools of individuals corresponding to each population to be sequenced. Additional details about DNA extraction are provided in Appendix S1.

Kurland S., Rafati N., Ryman N, & Laikre L. (2022). Genomic dynamics of brown trout populations released to a novel environment. Ecology and Evolution, 12(7), e9050.

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Genomic DNA Extraction and Sequencing

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Total genomic DNA was extracted and purified using the KingFisher Cell and Tissue DNA kit (Thermo Fisher Scientific) in a robotic KingFisher Flex Magnetic Particle Processor (Thermo Fisher Scientific) workstation.
Total genomic DNA was used as input material for library construction. DNA libraries were prepared using the Nextera XT library construction protocol and index kit (Illumina) and sequenced on a MiSeq Sequencer (Illumina) using MiSeq Reagent Kits v3 (600 cycles).

Gencay Y.E., Jasinskytė D., Robert C., Semsey S., Martínez V., Petersen A.Ø., Brunner K., de Santiago Torio A., Salazar A., Turcu I.C., Eriksen M.K., Koval L., Takos A., Pascal R., Schou T.S., Bayer L., Bryde T., Johansen K.C., Bak E.G., Smrekar F., Doyle T.B., Satlin M.J., Gram A., Carvalho J., Jessen L., Hallström B., Hink J., Damholt B., Troy A., Grove M., Clube J., Grøndahl C., Haaber J.K., van der Helm E., Zdravkovic M, & Sommer M.O. (2023). Engineered phage with antibacterial CRISPR–Cas selectively reduce E. coli burden in mice. Nature Biotechnology, 42(2), 265-274.

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Automated DNA Extraction from Tissue

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DNA was extracted from a 200 μL aliquot and remaining volumes were stored at −80°C. DNA extractions were automated using the KingFisher Flex System in conjunction with the KingFisher Cell and Tissue DNA Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.

Miller H.K., Branan M., Priestley R.A., Álvarez-Alonso R., Cherry C., Smith C., Urie N.J., Wiedenheft A., Bliss C., Marshall K, & Kersh G.J. (2024). Coxiella burnetii in domestic doe goats in the United States, 2019–2020. Frontiers in Veterinary Science, 11, 1393296.

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Genomic DNA Sequencing of Bt/Bc Isolates

Cited 2 times

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The genomic DNA of 78 Bt/Bc isolates was extracted and sequenced as described in Bonis et al. [17 (link)]. Briefly, the KingFisher Cell and Tissue DNA kit (Thermo Fisher Scientific, Waltham, MA, USA) was used to isolate genomic DNA. DNA purity and concentration were determined using a Nanodrop Spectrophometer and a Qubit fluorimeter, respectively. Global DNA integrity was visualized on a 0.8% agarose gel (Seakem GTG™ Agarose) after migration for 2 h at 90 V. Library preparation was carried out using the Nextera XT DNA Library Prep kit (Illumina, San Diego, CA, USA) and 150 bp paired-end sequencing of isolated DNA was performed by the Institut du Cerveau et de la Moëlle epinière, using a Nextseq500 sequencing system (Illumina). An in-house workflow called ARtWORK v1.0 [17 (link),31 (link)] was used to assemble reads with default parameters. The paired-end reads of the isolates are available in the PRJNA781790 BioProject on NCBI and the associated accession numbers are listed in Supplementary Table S1.

Fichant A., Felten A., Gallet A., Firmesse O, & Bonis M. (2022). Identification of Genetic Markers for the Detection of Bacillus thuringiensis Strains of Interest for Food Safety. Foods, 11(23), 3924.

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Linked-read Sequencing for N. phaeopus Genome

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We obtained a sample of N. phaeopus (ZMUC 112728) from the Natural History Museum of Denmark, Copenhagen, for reference genome assembly. Its genomic DNA was extracted using the KingFisher Duo Prime Magnetic Particle Processor (Thermo Fisher Scientific, USA) and the KingFisher Cell and Tissue DNA Kit (Thermo Fisher Scientific). A linked-read sequencing library was prepared using the Chromium Genome library kits (10 X Genomics) and sequenced on one Illumina Hiseq X lane at SciLifeLab Stockholm (Sweden). The de novo assembly analysis was performed using 10 X Chromium Supernova (v. 2.1.1). Reads were filtered for low quality and duplication, while assemblies were checked for accuracy and coverage and the best assembly was selected based on the highest genome coverage with the fewest errors. The final genome had a size of 1.12 Gb at a coverage of 50 X with N50=3504.2 kbp.

Tan H.Z., Jansen J.J., Allport G.A., Garg K.M., Chattopadhyay B., Irestedt M., Pang S.E., Chilton G., Gwee C.Y, & Rheindt F.E. (2023). Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds. eLife, 12, e85422.

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Quantification of Coxiella burnetii DNA

Cited 1 time

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C. burnetii DNA was extracted from murine tissues as previously described, with the following changes [11 (link)]. DNA extractions were performed using the KingFisher Flex System in conjunction with the KingFisher Cell and Tissue DNA Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Quantitative PCR was performed and reported as previously described [11 (link)].

Miller H.K., Priestley R.A, & Kersh G.J. (2021). Comparison of three Coxiella burnetii infectious routes in mice. Virulence, 12(1), 2562-2570.

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Quantifying Mitochondrial DNA Levels

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RNA was isolated from harvested cells using RNeasy Micro Kit (QIAGEN). cDNA synthesis was done following the manufacturer protocol (Maxima First Strand cDNA Synthesis Kit, Thermo Scientific, K1671). For mitochondrial DNA level determination, DNA was purificated using the KingFisher Cell and Tissue DNA Kit (Thermo). Real-time PCR was performed using a SYBR Green qPCR master mix (Takara) according to the manufacturer's protocol. The primers for the qRT-PCR are listed in Supplementary Table 1. All data were normalized to the control using Actin or RPLPO as internal control.

Wang Z., Chen L., Huang Y., Luo M., Wang H., Jiang Z., Zheng J., Yang Z., Chen Z., Zhang C., Long L., Wang Y., Li X., Liao F., Gan Y., Luo P., Liu Y., Wang Y., X.u.T.a.n., Zhou Z., Zhang A, & Shi C. (2021). Pharmaceutical targeting of succinate dehydrogenase in fibroblasts controls bleomycin-induced lung fibrosis. Redox Biology, 46, 102082.

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Extraction of High-Molecular-Weight DNA

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We also used the Qiagen MagAttract HMW DNA kit (cat no. 67563) and the KingFisher Cell and Tissue DNA kit (Thermo Scientific; cat no. 97030196), following the manufacturers’ guidelines. These protocols yielded HMW DNA ranging from 30 to 50 kb. The Genomic Tip (Qiagen) kit was also used for tissue-based extraction of HMW DNA.

Rhie A., McCarthy S.A., Fedrigo O., Damas J., Formenti G., Koren S., Uliano-Silva M., Chow W., Fungtammasan A., Kim J., Lee C., Ko B.J., Chaisson M., Gedman G.L., Cantin L.J., Thibaud-Nissen F., Haggerty L., Bista I., Smith M., Haase B., Mountcastle J., Winkler S., Paez S., Howard J., Vernes S.C., Lama T.M., Grutzner F., Warren W.C., Balakrishnan C.N., Burt D., George J.M., Biegler M.T., Iorns D., Digby A., Eason D., Robertson B., Edwards T., Wilkinson M., Turner G., Meyer A., Kautt A.F., Franchini P., Detrich HW I.I.I., Svardal H., Wagner M., Naylor G.J., Pippel M., Malinsky M., Mooney M., Simbirsky M., Hannigan B.T., Pesout T., Houck M., Misuraca A., Kingan S.B., Hall R., Kronenberg Z., Sović I., Dunn C., Ning Z., Hastie A., Lee J., Selvaraj S., Green R.E., Putnam N.H., Gut I., Ghurye J., Garrison E., Sims Y., Collins J., Pelan S., Torrance J., Tracey A., Wood J., Dagnew R.E., Guan D., London S.E., Clayton D.F., Mello C.V., Friedrich S.R., Lovell P.V., Osipova E., Al-Ajli F.O., Secomandi S., Kim H., Theofanopoulou C., Hiller M., Zhou Y., Harris R.S., Makova K.D., Medvedev P., Hoffman J., Masterson P., Clark K., Martin F., Howe K., Flicek P., Walenz B.P., Kwak W., Clawson H., Diekhans M., Nassar L., Paten B., Kraus R.H., Crawford A.J., Gilbert M.T., Zhang G., Venkatesh B., Murphy R.W., Koepfli K.P., Shapiro B., Johnson W.E., Di Palma F., Marques-Bonet T., Teeling E.C., Warnow T., Graves J.M., Ryder O.A., Haussler D., O’Brien S.J., Korlach J., Lewin H.A., Howe K., Myers E.W., Durbin R., Phillippy A.M, & Jarvis E.D. (2021). Towards complete and error-free genome assemblies of all vertebrate species. Nature, 592(7856), 737-746.

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Extraction and Analysis of Tumor Nucleic Acids

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Nucleic acids were extracted using pleural fluid (Patient B and D) or formalin-fixed, paraffin-embedded (FFPE) samples (Patient A and C) from patient tumors and fresh frozen tumors from PDX tumors. Genetic analysis was performed using patient tumors and PDX tumors of TG1, TG2, and TG3 in LC-001 to LC-003, patient tumors and PDX tumors of TG1 in LC-004, and patient tumors and PDX tumors of TG1 and TG2 in LC-005. DNA and RNA were extracted from FFPE samples using a GeneRead DNA FFPE Kit (Qiagen) and an RNeasy FFPE Kit (Qiagen), and from pleural fluid and fresh frozen tumors using either a KingFisher Cell and Tissue DNA Kit (Thermo Fisher Scientific) or a MagMAX mirVana Total RNA Isolation Kit (Thermo Fisher Scientific).

Jo H., Yagishita S., Hayashi Y., Ryu S., Suzuki M., Kohsaka S., Ueno T., Matsumoto Y., Horinouchi H., Ohe Y., Watanabe S.I., Motoi N., Yatabe Y., Mano H., Takahashi K, & Hamada A. (2022). Comparative Study on the Efficacy and Exposure of Molecular Target Agents in Non-small Cell Lung Cancer PDX Models with Driver Genetic Alterations. Molecular cancer therapeutics, 21(2).

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Museum Specimen DNA Extraction and Sequencing

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We extracted genomic DNA from toepad samples (n = 59) and from fresh blood and tissue samples (n = 19). Protocol for DNA extraction from toepad samples followed Irestedt et al. (2006) . We followed the protocol of Meyer and Kircher (2010) (link) to create sequencing libraries suitable for Illumina sequencing of toepad DNA extracts. Library preparation included blunt-end repair, adapter ligation, and adapter fill-in, followed by four independent index PCRs. The libraries were run on half a lane on Illumina HiSeq X, pooled at equal ratio with other museum samples. Genomic DNA was extracted from fresh samples with KingFisher Duo magnetic particle processor (ThermoFisher Scientific) using the KingFisher Cell and Tissue DNA Kit.
Library preparation, using Illumina TruSeq DNA Library Preparation Kit, and sequencing on Illumina HiSeqX (2x151 bp) was performed by SciLifeLab. All raw reads generated for this study have been deposited at the NCBI Sequence Read Archive (SRA), accession number [pending] .

Reeve A.H., Gower G., Pujolar J.M., Smith B.T., Petersen B., Olsson U., Haryoko T., Koane B., Maiah G., Blom M.P.K., Ericson P.G.P., Irestedt M., Racimo F., & Jønsson K.A. (2022). Population genomics of the island thrush elucidates one of earth’s great archipelagic radiations.

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