Genomic tip kit

Manufactured by Qiagen

Sourced in Germany, United States, United Kingdom, China

The Genomic-tip kit is a laboratory equipment product designed for the purification of high-quality genomic DNA from a variety of sample types. It utilizes a silica-based anion-exchange resin to selectively bind and purify DNA, providing a simple and efficient method for DNA extraction.

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Lab products found in correlation

Hiseq 2000, by Illumina (5 mentions) Dnbseq g400, by MGI Tech (4 mentions) Proteinase k, by Qiagen (3 mentions) Nextseq 500, by Illumina (3 mentions) Buffer qbt, by Qiagen (2 mentions) Miseq sequencer, by Illumina (2 mentions) Hiseq 2500, by Illumina (2 mentions) Ampure xp bead, by Beckman Coulter (2 mentions) Genomic tip protocol, by Qiagen (2 mentions) Hiseq 2500 rapid flow cell, by Illumina (2 mentions) Rapid sequencing kit, by Oxford Nanopore (2 mentions) Flow cell version flo min107 r9, by Oxford Nanopore (2 mentions) Guppy v2, by Oxford Nanopore (2 mentions) Dneasy plant mini kit, by Qiagen (2 mentions) Smrtbell express template prep kit, by Pacific Biosciences (2 mentions) Migseq 2000 dna sequencer, by MGI Tech (2 mentions) Nanodrop spectrophotometer, by Thermo Fisher Scientific (2 mentions) Picogreen reagent, by Thermo Fisher Scientific (2 mentions) Genomic dna buffer, by Qiagen (2 mentions) Xhoi restriction endonuclease, by New England Biolabs (2 mentions)

Close spelling variants of this product

QIAGEN Blood & Cell Culture DNA Kit with 100/G Genomics-tips Genomic-Tips 100/G kit Genomic-tip 20/G kit Genomic-tip 100/G kit Genomic-tip 20/G isolation kit DNA Genomic-tip kit Genomic-tip 100 G−1 kit QIAGEN Genomic Tip and Genomic DNA Buffer Set Kit Genomic-tip 500/G kit Genomic-Tip 20 Kit

44 protocols using genomic tip kit

Sequencing of Candida orthopsilosis

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For Illumina sequencing, the 27 C. orthopsilosis isolates were cultured overnight in a shaking incubator at 30°C in 5 ml YPD medium (1% yeast extract, 2% peptone, 2% glucose). Genomic DNA was extracted using the Qiagen Genomic Tip-kit (20/G, product code 10223).
For PacBio sequencing, Sample 427 was grown in 100 ml synthetic complete media (2% glucose, 6.7% yeast nitrogen base, 2% Bacto agar, 0.2% dropout mix) overnight to reduce the carbohydrate concentrations. DNA was extracted using the Qiagen Genomic-tip kit (500/G, product code 10262) using a modified protocol for yeast (available at PacBio SampleNet, www.pacbiosamplenet.com).

Schröder M.S., Martinez de San Vicente K., Prandini T.H., Hammel S., Higgins D.G., Bagagli E., Wolfe K.H, & Butler G. (2016). Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species. PLoS Genetics, 12(11), e1006404.

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Polysaccharide-rich DNA Extraction from D. molle

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Extraction of DNA from D. molle samples E11-036 and E11-037 was complicated by the presence of copious amounts of polysaccharide-rich mucus. We utilized a protocol previously adapted from Sokolov for the precipitation of polysaccharides found in marine invertebrate slime.^{51 ,52 (link)} Briefly, tissue was sliced thinly and squashed between two aluminum foil sheets, then treated with proteinase K (Qiagen). Polysaccharides and proteins were then precipitated with saturated KCl. Additional KCl was required beyond what was called for in the original protocol. Samples were centrifuged and an equal volume of isopropanol added to the supernatant. White precipitate formed upon incubation at room temperature. The mixture was centrifuged again and the pellet washed with 70% ethanol. Excess solvent was removed by air drying and the pellet resuspended in QBT buffer (Qiagen). From this point forward, DNA extraction followed the standard protocol for the Qiagen Genomic-tip kit. An Illumina library was prepared using the E11-036 DNA with ~700 bp insert sizes and then sequenced on an Illumina MiSeq sequencer using a 250 bp paired end run. For D. molle sample E11-037, a 350 bp insert size library was prepared and sequenced (100 bp paired end) on an Illumina HiSeq 2500.

Smith T.E., Pond C.D., Pierce E., Harmer Z.P., Kwan J., Zachariah M.M., Harper M.K., Wyche T.P., Matainaho T.K., Bugni T.S., Barrows L.R., Ireland C.M, & Schmidt E.W. (2018). Accessing chemical diversity from the uncultivated symbionts of small marine animals. Nature chemical biology, 14(2), 179-185.

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Sequencing and Methylation of C. thermocellum

Cited 1 time

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Genomic DNA from C. thermocellum ATCC 27405 was isolated using the Genomic Tip kit (Qiagen according to the manufacturer’s instructions and sent to Expression Analysis (Durham, NC, USA) for sequencing on a Pacific Biosciences (PacBio) instrument. Single-molecule real-time (SMRT) sequencing was performed using the PacBio RS technology with four SMRT cells. Methylated sequences were determined by Expression Analysis using the SMRT Analysis software [10 (link)].

Riley L.A., Ji L., Schmitz R.J., Westpheling J, & Guss A.M. (2019). Rational development of transformation in Clostridium thermocellum ATCC 27405 via complete methylome analysis and evasion of native restriction–modification systems. Journal of Industrial Microbiology & Biotechnology, 46(9), 1435-1443.

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Bulk Segregant Analysis for Genetic Mapping

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Genomic DNA was extracted using the Qiagen Genomic-tip kit. DNA of the pooled segregants was sequenced using Illumina Hiseq 2000. Detailed procedures of DNA preparation were described previously46 (link). We used paired-end libraries, 101 bp per read, the coverage was ∼50 × . Reads were aligned to the S288c genome using BWA with ‘-n 5 -o 2' options. Single-nucleotide polymorphism (SNP) calling was done using SAMtools47 (link). The allele frequency of S288c was scored at each polymorphic position. As indicated by the segregation pattern, two genomic regions enriched for each parental strain are expected. We defined the region involved in the YJM421 parent as the genomic region comprising most of the mapped SNPs with allele frequency of S288c <0.1, as the S288c alleles were supposed to be absent (chromosome V). As for the region involved in the S288c genome, the YJM421 alleles should have been absent, which would result in a region with no mapped SNP markers (chromosome X). Inconsecutive SNPs that showed high allelic enrichment are considered to be sequencing noise and were not considered in the analysis.

Hou J., Friedrich A., Gounot J.S, & Schacherer J. (2015). Comprehensive survey of condition-specific reproductive isolation reveals genetic incompatibility in yeast. Nature Communications, 6, 7214.

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Generating High-Quality Whole-Genome Sequence Libraries

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Whole-genome sequence libraries (Supplementary Table 19) were generated from genomic DNA extracted from a single adult female O. volvulus worm and a single adult female O. ochengi worm, both washed thoroughly in 0.1 M EDTA. DNA was extracted using the Qiagen Genomic-tip kit. The ratio of host to parasite DNA was examined by qPCR using single-copy genes as markers. PCR-free 400–550 bp paired-end Illumina libraries were produced (one library per species) using a protocol based on a previously described method^{56 (link)} but using Agencourt AMPure XP beads for sample clean-up and size selection. Genomic DNA was precipitated onto beads after each enzymatic stage with an equal volume of 20% polyethylene glycol 6000 and 2.5 M sodium chloride solution. Beads were not separated from the sample throughout the process until after the adapter ligation stage. Fresh beads were then used for size selection. O. volvulus genomic DNA was used to generate a 3 kb mate pair library using a modified SOLiD 5500 protocol adapted for Illumina sequencing⁵⁷.

Cotton J.A., Bennuru S., Grote A., Harsha B., Tracey A., Beech R., Doyle S.R., Dunn M., Dunning Hotopp J.C., Holroyd N., Kikuchi T., Lambert O., Mhashilkar A., Mutowo P., Nursimulu N., Ribeiro J.M., Rogers M.B., Stanley E., Swapna L.S., Tsai I.J., Unnasch T.R., Voronin D., Parkinson J., Nutman T.B., Ghedin E., Berriman M, & Lustigman S. (2016). The genome of Onchocerca volvulus, agent of river blindness. Nature microbiology, 2, 16216.

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PCR Amplification of Sf9 Genomic DNA

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PCR amplifications were performed using Sf9 genomic DNA as a template. DNA was isolated as described above using the Genomic-Tip Kit (QIAGEN) and resuspended in water. PCR amplifications were carried out in a final volume of 50 µl containing 10 µl of 5X Phusion DNA polymerase buffer (HF buffer) (Finnzymes, Finland), 1 µl of 10 mM each dNTP (Biolabs), 0.5 µmoles of each primer (Table S1; Cloning of introns), 1 unit of Phusion DNA Polymerase and 200 ng of Sf9 genomic DNA. After denaturation at 98°C for 2 min, a two-step protocol was used with (i) seven cycles of amplification in the following conditions: denaturation at 98°C for 15 sec, annealing and extension for 3 minutes at 72°C and (ii) thirty cycles of amplification with denaturation at 98°C for 15 sec, annealing and extension for 5 min at 68°C. PCR products were isolated on agarose gels (SeaKem GTG, Lonza) and purified with the QIAquick Gel Extraction Kit (QIAGEN). PCR fragments were then adenylated with Taq Polymerase as described above and cloned in pGEM-T Easy (Promega) for sequencing analysis (Operon Eurofins MWG, Germany).

Juliant S., Harduin-Lepers A., Monjaret F., Catieau B., Violet M.L., Cérutti P., Ozil A, & Duonor-Cérutti M. (2014). The α1,6-Fucosyltransferase Gene (fut8) from the Sf9 Lepidopteran Insect Cell Line: Insights into fut8 Evolution. PLoS ONE, 9(10), e110422.

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Genomic DNA and RNA Extraction from Sf9 Cells

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High molecular weight genomic DNA was extracted from Sf9 cells (15×10⁶ cells) using the Genomic-Tip Kit (QIAGEN) as recommended by the manufacturer. Total cytoplasmic RNA was extracted from 2×10⁷Sf9 cells using a method previously described [59] (link). After precipitation, RNA pellets were washed with a cold solution containing 75% ethanol and 25% sodium acetate and resuspended in 50 µl of distilled water. Fifty µg of RNA were then incubated with 15 units of RNase-free DNase I (New England Biolabs) at 37°C for 20 min and then the DNase was inactivated with 5 mM EDTA at 75°C for 10 min. RNA samples were loaded on an RNeasy column (QIAGEN) as recommended by the manufacturer. Purified RNA was immediately stored at −80°C.

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Genome sequencing of P. aeruginosa isolate

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The isolate DHS01, the first isolate of the epidemic, was isolated in May 1997 from the nose of a 31-year-old male patient in the surgical intensive care unit in the University Hospital of Besançon (Eastern France). In our hospital, P. aeruginosa is searched for weekly in patients hospitalized in the intensive care unit. Microbiological records revealed that the patient was already colonized by P. aeruginosa 25 days before isolation of DHS01. DHS01 was identified at the species level by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) with a Microflex LT (Bruker Daltonik), according to the manufacturer's procedures. Bacterial DNA was isolated from an overnight culture on Mueller-Hinton (MH) agar using a Genomic-tip kit (Qiagen) and further sequenced with Single Molecule Real-Time technology (Pacific Biosciences) [11 (link)]. The reads were assembled using Hgap3 into a circular complete genome [12 (link)]. The genome was annotated using the National Center for Biotechnology Information (NCBI) Prokaryotic Genome Annotation Pipeline (pgat) [13 (link)]. The genes were sorted as core or accessory genes of the species P. aeruginosa by comparing to previous pangenome analysis [14 (link)].

Petitjean M., Martak D., Silvant A., Bertrand X., Valot B, & Hocquet D. (2017). Genomic characterization of a local epidemic Pseudomonas aeruginosa reveals specific features of the widespread clone ST395. Microbial Genomics, 3(10), e000129.

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Metagenomic DNA Extraction from Sponge Samples

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Metagenomic DNA was extracted from each RNALater preserved sponge sample using the Genomic Tip Kit (Qiagen, MD, USA) with some modifications. The sponge tissue (~1 cm³) was flash frozen in liquid nitrogen and homogenized using a sterile pestle in a conical tube. Buffer B1 (3.5 mL) containing Rnase A (0.2 mg mL⁻¹) was then added and further homogenization was done. The solution was then treated with proteinase K (0.5 mg mL⁻¹) and lysozyme (2.5 mg mL⁻¹) for 5 hours at 37 °C while shaking gently. Buffer B2 (1.2 mL) was added and the solution was further incubated at 50 °C for 30 minutes. Samples were then centrifuged and the supernatant was treated according to the Genomic Tip protocol (Qiagen, MD, USA). Metagenomic DNA was mechanically sheared to an average size of ~500 bps, and Illumina sequencing libraries were prepared using Apollo 324™ NGS Library Prep System and the PrepX DNA library kit (Wafergen, CA) and sequenced on an Illumina HiSeq 2500 Rapid Flow cell as paired-end 2×175 bps reads for Ren-PNG-07113, Ren-Pal-02, and Ren-Bali-16–03, and 2×141 bps for Ren-PNG-07060 (Supplementary Table 1).

Tianero-McIntosh M.D., Balaich J.N, & Donia M.S. (2019). Localized production of defense chemicals by intracellular symbionts of Haliclona sponges. Nature microbiology, 4(7), 1149-1159.

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Genome Assembly of Pisum sativum Line JI128

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DNA was extracted from the leaves of JI128 plants using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany). Short-read DNA sequencing libraries were prepared according to the manufacturer’s instructions, and sequenced on DNA sequencers, NextSeq 500 (Illumina) and DNBSEQ-G400 (MGI Tech, Shenzhen, China). The genome size of line JI128 was estimated by k-mer distribution analysis using the Jellyfish software (Marcais and Kingsford 2011 (link)).
High-molecular-weight DNA was extracted from JI128 DNA using the Genomic-tip kit (Qiagen), and a long-read sequence library was constructed using the Rapid Sequencing Kit (version SQK-RAD004) (Oxford Nanopore Technologies, Oxford, UK). The library was sequenced with the MinION using flow cell version FLO-MIN107 R9 (Oxford Nanopore Technologies). Base calling from the FAST5 files was performed using Guppy v2.3.5 (Oxford Nanopore Technologies). Long reads were assembled with wtdbg2 v2.2 (Ruan and Li 2020 (link)), and potential sequencing errors in the contigs were corrected only once using Pilon (Walker et al. 2014 (link)). The resulting genome assembly was designated as PSA_r1.0. Assembly completeness was evaluated with the embryophyta_odb10 data using Benchmarking Universal Single-Copy Orthologs (BUSCO) v3.0.2 (Simao et al. 2015 (link)).

Shirasawa K., Sasaki K., Hirakawa H, & Isobe S. (2021). Genomic region associated with pod color variation in pea (Pisum sativum). G3: Genes|Genomes|Genetics, 11(5), jkab081.

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