Genomic tip 100 kit

Manufactured by Qiagen

Sourced in United States

The Genomic Tip-100 kit is a laboratory equipment product manufactured by Qiagen. The kit is designed for the purification of genomic DNA from a variety of sample types, including cells, tissues, and microorganisms. The kit utilizes anion-exchange chromatography to selectively bind and purify genomic DNA, providing a reliable and efficient method for DNA extraction and preparation.

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Lab products found in correlation

Rapid barcoding kit, by Oxford Nanopore Technologies (1 mentions) Nextera xt dna library preparation kit, by Illumina (1 mentions) Clc genomics workbench v20, by Qiagen (1 mentions) Smrtbell express template prep kit 2, by Pacific Biosciences (1 mentions) Genome analyzer iix, by Illumina (1 mentions) Genejet plasmid miniprep kit, by Thermo Fisher Scientific (1 mentions) Genejet gel extraction kit, by Thermo Fisher Scientific (1 mentions) Redtaq ready mix pcr mix, by Merck Group (1 mentions) Phusion high fidelity dna polymerase, by Thermo Fisher Scientific (1 mentions) Mycycler, by Bio-Rad (1 mentions)

Close spelling variants of this product

Genomic-tip (58 citations) Genomic-tip kit (44 citations) QIAGEN® Genomic kits (2 citations) QIAGEN Blood & Cell Culture DNA Kit with 100/G Genomics-tips (2 citations)

6 protocols using genomic tip 100 kit

Isolation and Identification of Bacteria from Douchi

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The dry Douchi samples obtained from Jiatai Co., Ltd., Chongqing, China were soaked in sterile saline for 20 min at 37 °C, treated at 80 °C for 10 min, and isolated by serial dilution in sterile saline. After centrifugation at 4,000 rpm for 5 min, the culture supernatants were cultured on the nutrient agar broth containing casein at 37 °C for 18 h, followed by collecting the single colonies and culture in Luria-Bertani medium at 37 °C for 72 h under shaking.
The physiological and biochemical characteristics of the isolates were identified as described in the Bergey’s Brochure for identification of Bacteriology. The extraction of total genomic DNA was performed using the Genomic Tip-100 kit (Qiagen, Hilden, Germany) for 16 S rDNA identification, and the gene was PCR amplified using primers of 5′-AGAGTTTGATCCTGGCTCAG-3′ and 5′-ACGGCTACCTTGTTACGACT-3′ ^{26 (link)}. The 16S rDNA sequence homology analysis was performed using the basic local alignment search tool (BLAST) at the website of NCBI (http://www.ncbi.nlm.nih.gov).

Hu Y., Yu D., Wang Z., Hou J., Tyagi R., Liang Y, & Hu Y. (2019). Purification and characterization of a novel, highly potent fibrinolytic enzyme from Bacillus subtilis DC27 screened from Douchi, a traditional Chinese fermented soybean food. Scientific Reports, 9, 9235.

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Sequencing and Assembly of Bacterial Genomes

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Transconjugants were sequenced by a combination of Oxford Nanopore and Illumina MiSeq technologies. Complete genomic DNA (gDNA) was purified using the Qiagen Genomic-Tip 100 kit according to the manufacturer’s directions. Library preparations for Nanopore sequencing were performed with the Rapid barcoding kit (Nanopore) according to the manufacturer’s recommendations. Multiplexed libraries were concentrated using AMPure XP beads (Nanopore) and sequenced in a flow cell until no active pores remained. MiSeq libraries were prepared and sequenced by 300-bp paired-end read lengths using a Nextera XT DNA library preparation kit (Illumina) according to the manufacturer’s instructions. De novo assembly of the Nanopore data was performed using the long-read support function in CLC Genomics Workbench v.20 (Qiagen). Contigs were reanalyzed by reference assembly using MiSeq data with CLC Genomics Workbench v.20 including the Microbial Analysis Pro suite (Qiagen). Detection of resistance genes and plasmid replicons was done by submitting de novo-assembled contigs to the online resources ResFinder (66 (link)) and PlasmidFinder (67 (link)), respectively, at the Center for Genomic Epidemiology, DTU, Denmark.

Rajer F, & Sandegren L. (2022). The Role of Antibiotic Resistance Genes in the Fitness Cost of Multiresistance Plasmids. mBio, 13(1), e03552-21.

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Larval Genomic DNA Extraction and PacBio Sequencing

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Genomic DNA was isolated from 24 snap-frozen pooled male and female larvae using the Qiagen Genomic tip 100 kit (Qiagen, Germantown, MD, USA). DNA isolation and library preparation using SMRTbell Express Template Prep Kit 2.0 (Pacific Biosciences, Menlo Park, CA, USA) were performed by the sequencing provider. PacBio HiFi sequencing was performed at DNA Sequencing Centre (DNASC) at Brigham Young University (Provo, UT, USA) using the Sequel II System machine. The sequencing resulted in 1,617,087 HiFi reads with a total length of 23.8 Mb. The quality of HiFi reads was assessed with FastQC, and no remaining adapters or specific overrepresented sequences were found.

Volarić M., Despot-Slade E., Veseljak D., Meštrović N, & Mravinac B. (2022). Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani. International Journal of Molecular Sciences, 23(11), 5869.

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Whole Genome Sequencing of Yeast Strains

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Whole genome sequences of strains B-1A and G-4A were obtained by using Illumina pair-end sequencing. Briefly, genomic DNA was extracted from a saturated culture of 100 ml under anaerobic condition (YPD) using the genomic tip-100 kit (Qiagen, Courtaboeuf, FRANCE). Paired-end Illumina sequencing libraries were prepared from sonicated genomic DNA according to manufacturer protocols (Genomic DNA Sample Preparation) and were realized by the Genomic and Transcriptomic Facility of Bordeaux, FRANCE. Sequencing was performed on Illumina Genome Analyzer IIx (Illumina, Palo Alto, CA) with a read length of 54 bp. Raw reads data have been deposited in the SRA at NCBI with the accession number PRJNA419624. The genome coverage was respectively 45X and 34X for B-1A and G-4A, respectively. After reads quality trimming and filtration step, each strain was aligned to the reference genome of Saccharomyces cerevisiae S288c (version Apr2011/sacCer3) using “Bowtie2” with default parameters. Single Nucleotide Polymorphisms (SNPs) were called using Samtools mpileup with mapping quality ≥ 30, base quality ≥ 20, and varFilter depth ≥ 10. Single amino-acid polymorphisms were identified using snpEff [65 (link)] requiring quality QUAL ≥30 and genotype GEN[*] GQ ≥ 20. Using this procedure, we defined a set of 9829 high-quality SNP (Q > 30, homozygous) named WGS-SNP and given in (Additional file 4).

Marullo P., Durrens P., Peltier E., Bernard M., Mansour C, & Dubourdieu D. (2019). Natural allelic variations of Saccharomyces cerevisiae impact stuck fermentation due to the combined effect of ethanol and temperature; a QTL-mapping study. BMC Genomics, 20, 680.

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Genomic DNA Isolation and Genetic Manipulation

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All enzymes were purchased from Thermo Scientific. Genomic DNA of P. alvei CCM 2051^T was isolated by using a Genomic Tip 100 kit (Qiagen) according to the manufacturer’s instructions, except that cells were broken by repeated freezing and thawing cycles (10 times) (Zarschler et al. 2009 (link)). The GeneJET™ Gel Extraction Kit (Fermentas) was used to purify DNA fragments from agarose gels and to purify digested plasmids and oligonucleotides. Plasmid DNA from transformed cells was isolated with the GeneJET™ Plasmid Miniprep kit (Fermentas). Agarose gel electrophoresis was performed as described elsewhere (Sambrook et al. 1989 ). Primers for PCR and DNA sequencing were purchased from Invitrogen (Table III). PCR was performed using the Phusion^® High-Fidelity DNA Polymerase (Fermentas) and the thermal cycler My CyclerTM (Bio-Rad). Transformation of chemically competent E. coli DH5α cells and E. coli BL21 (DE3) cells was done according to the manufacturer’s protocol (Invitrogen). Transformation of P. alvei CCM 2051^T wild type, P. alvei CCM 2051^T ΔwsfP, P. alvei CCM 2051^T ΔPAV2c_01630 and P. alvei CCM 2051^T ΔPAV2c_01640 cells is described elsewhere (Zarschler et al. 2009 (link)). Transformants were screened by PCR using RedTaq ReadyMix PCR mix (Sigma-Aldrich), and recombinant clones were analyzed by restriction mapping and confirmed by sequencing (Microsynth).

Janesch B., Schirmeister F., Maresch D., Altmann F., Messner P., Kolarich D, & Schäffer C. (2015). Flagellin glycosylation in Paenibacillus alvei CCM 2051T. Glycobiology, 26(1), 74-87.

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Antarctic Krill Genome Sequencing

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Our experimental procedures complied with the current laws on animal welfare and research in China. Alive Antarctic krill specimens were collected from the Argentine Sea area (45°92’S,61°82’W). Genomic DNAs were extracted from the whole bodies of pooled specimens with a Qiagen GenomicTip100 kit (Qiagen, Germanton, MD, USA) according to the manufacturer’s protocol. With the traditional whole-genome shotgun sequencing strategy [14 (link)], we used 1 μg of normalized DNA to prepare a paired-end short-insert library (400 bp). Quantification and size estimations of the library were performed on a Zebra Flowcell 3.1 chip. Finally, the library was normalized to 15 ng/μL for paired-end sequencing (100 bp in length) on a BGISeq500 platform (BGI, Shenzhen, China). Raw genome sequencing reads have been deposited in the NCBI and China National GeneBank (CNGB) under the project IDs PRJNA598052 and CNP0000808, respectively.

Huang Y., Bian C., Liu Z., Wang L., Xue C., Huang H., Yi Y., You X., Song W., Mao X., Song L, & Shi Q. (2020). The First Genome Survey of the Antarctic Krill (Euphausia superba) Provides a Valuable Genetic Resource for Polar Biomedical Research. Marine Drugs, 18(4), 185.

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