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Gentra puregene dna extraction kit

Manufactured by Qiagen
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The Gentra Puregene DNA extraction kit is a laboratory equipment used for the isolation and purification of genomic DNA from a variety of biological samples, including cells, tissues, and blood. It utilizes a reliable and efficient process to extract high-quality DNA suitable for downstream applications such as PCR, sequencing, and other molecular biology techniques.

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Lab products found in correlation

Ez dna methylation kit, by Zymo Research (6 mentions) Rneasy fibrous tissue mini kit, by Qiagen (2 mentions) Cd45 macs microbeads, by Miltenyi Biotec (2 mentions) 850 k infiniummethylationepic beadchip, by Illumina (2 mentions) Nanodrop, by Thermo Fisher Scientific (2 mentions) Nanodrop 2000 spectrophotometer, by Thermo Fisher Scientific (2 mentions) Miseq v3, by Illumina (1 mentions) Abi 3730xl dna analyzer, by Thermo Fisher Scientific (1 mentions) Nextera rapid capture exome kit, by Illumina (1 mentions) Sureselectxt human all exon v6, by Agilent Technologies (1 mentions) Sureselectxt reagent kit, by Agilent Technologies (1 mentions) Dneasy blood tissue kit, by Qiagen (1 mentions) Hiseq 2000, by Illumina (1 mentions) Truseq nano dna ht sample prep kit, by Illumina (1 mentions) Sureselect human all exon kit, by Agilent Technologies (1 mentions) Novaseq 6000 platform, by Illumina (1 mentions) Infinium methylationepic array, by Illumina (1 mentions) Ez 96 dna methylation kit, by Zymo Research (1 mentions) Ez dna kit, by Zymo Research (1 mentions) Cviaii, by New England Biolabs (1 mentions)

32 protocols using gentra puregene dna extraction kit

1

Genome Sequencing of Pigment Mutants

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Genomic DNA was extracted from bacterial strains of interest using a Gentra PureGene DNA extraction kit (QIAGEN) with isolated DNA re-suspended in sterile water. Paired end sequencing was conducted by Eurofins Genomics using Illumina MiSeq V3 with 2 × 300 bp reads. Reads were mapped to the P. aeruginosa UCBPP-PA14 NC_008463.1 reference genome and delivered as BAM and BAI files. Further sequence analysis for SNP identification was conducted using the Integrative Genome Viewer software platform using the reference strain UCBPP-PA14 and the more recent PA14 Or genome sequence (NZ_LT608330.1). This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession SZXO00000000 (red pigmented mutant), SZXP00000000 (brown pigmented mutant), and SZXQ00000000 (yellow pigmented mutant).
Flynn S., Reen F.J, & O’Gara F. (2019). Exposure to Bile Leads to the Emergence of Adaptive Signaling Variants in the Opportunistic Pathogen Pseudomonas aeruginosa. Frontiers in Microbiology, 10, 2013.
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2

Verifying Wolbachia-free Nasonia Strains

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To confirm the uninfected Wolbachia status of the Nasonia strains used, DNA was extracted using the Gentra PureGene DNA extraction kit (QIAGEN®), as well as a control infected strain (N. vitripennis 12.1). Verification of infection status was performed using PCR with the primers ftsZuniF and fts2uniR as previously described [25 (link)]. Individual adult Nasonia, n = 4 UT, n = 3 R3, and n = 3 13.2, n = 3 Wolbachia positive Nasonia - strain 12.1, were tested and no Wolbachia was detected in the UT, R3, or 13.2 strains.
Saulsberry A., Pinchas M., Noll A., Lynch J.A., Bordenstein S.R, & Brucker R.M. (2017). Establishment of F1 hybrid mortality in real time. BMC Evolutionary Biology, 17, 37.
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3

Bile Acid and Microbiome Analysis in BALF

Cited 1 time
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A BALF supernatant aliquot from the two middle washes of the right middle lobe was centrifuged at 13,000 rpm for 10 min. Supernatants were profiled for 12 different bile acids as we previously described [14 (link)]. Microbial DNA was then extracted from the bacterial pellets using the Gentra PureGene DNA Extraction kit (QIAGEN) as per the manufacturer’s recommendations. To have an unbiased representation of the microbial DNA signatures in BALF, a minor modification was included, consisting of an overnight digestion with proteinase K.
Flynn S., Reen F.J., Caparrós-Martín J.A., Woods D.F., Peplies J., Ranganathan S.C., Stick S.M, & O’Gara F. (2020). Bile Acid Signal Molecules Associate Temporally with Respiratory Inflammation and Microbiome Signatures in Clinically Stable Cystic Fibrosis Patients. Microorganisms, 8(11), 1741.
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4

DNA Methylation Profiling from Peripheral Blood

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Peripheral blood samples were collected at the eighth examination samples (2005 to 2008). Genomic DNA was extracted from buffy coat using the Gentra Puregene DNA extraction kit (Qiagen) and bisulfite converted using EZ DNA Methylation kit (Zymo Research Corporation). DNA methylation quantification was conducted in two laboratory batches. Methylation beta values were generated using the Bioconductor minfi package with background correction. Sample exclusion criteria included poor SNP matching of control positions, missing rate >1%, outliers from multi-dimensional scaling (MDS), and sex mismatch. Probes were excluded if missing rate >20%. In total, 2,635 samples and 443,304 CpG probes remained for analysis.
Marioni R.E., Shah S., McRae A.F., Chen B.H., Colicino E., Harris S.E., Gibson J., Henders A.K., Redmond P., Cox S.R., Pattie A., Corley J., Murphy L., Martin N.G., Montgomery G.W., Feinberg A.P., Fallin M.D., Multhaup M.L., Jaffe A.E., Joehanes R., Schwartz J., Just A.C., Lunetta K.L., Murabito J.M., Starr J.M., Horvath S., Baccarelli A.A., Levy D., Visscher P.M., Wray N.R, & Deary I.J. (2015). DNA methylation age of blood predicts all-cause mortality in later life. Genome Biology, 16(1), 25.
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5

Transcriptomic Analysis of Canine Testicular Tissue

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Adult Golden Retriever testes were obtained from routine castration procedures. Tissue samples were flash-frozen in liquid nitrogen and stored at −80°C. Genomic DNA was extracted using a Gentra Puregene DNA extraction kit (Qiagen), and RNA was extracted using an RNeasy fibrous tissue mini kit (Qiagen). Library preparation and NovaSeq S4 Illumina paired-end sequencing were performed at the UC Davis Genome Center. Reads were aligned to the CanFam3.1 reference assembly using minimap2 (Li 2018 (link)). PCR duplicate reads were removed, and the aligned files were sorted and indexed using SAMtools (Danecek et al. 2021 (link)). Evidence for chimeric transcripts in the RNA-seq data set was found through visual analysis of the retroCNV insertion sites and nearby genes in IGV. Because of the small sample size and heterogeneity of retroCNVs between individuals, evidence of expression was determined visually through examination of the insert site, the 5′ UTR of the parent gene, and insertion site genes for chimeric transcripts. For retroCNVs that contained any retroCNV-specific variants, the parent gene loci were examined for evidence of the retroCNV-specific variant, which would indicate expression of the retroCNV. A minimum of two discordant reads was used to consider a retroCNV expressed.
Batcher K., Varney S., York D., Blacksmith M., Kidd J.M., Rebhun R., Dickinson P, & Bannasch D. (2022). Recent, full-length gene retrocopies are common in canids. Genome Research, 32(8), 1602-1611.
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6

Blood DNA Extraction

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DNA was extracted from peripheral blood EDTA samples using Gentra Puregene DNA Extraction kit (QIAGEN), according to the manufacturer's instructions.
Whitford W., Hawkins I., Glamuzina E., Wilson F., Marshall A., Ashton F., Love D.R., Taylor J., Hill R., Lehnert K., Snell R.G, & Jacobsen J.C. (2017). Compound heterozygous SLC19A3 mutations further refine the critical promoter region for biotin-thiamine-responsive basal ganglia disease. Cold Spring Harbor Molecular Case Studies, 3(6), a001909.
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7

Molecular Detection of Mycobacterium Ulcerans

Cited 2 times
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Whole genome DNA was extracted from clinical samples in CLS at KCCR or INH using the Gentra Puregene DNA extraction kit (Qiagen) with minor modifications of the manufacturer’s instructions as described in S1 Protocol [6 (link)]. DNA extracts were stored at 4–8°C (up to one week) or -18°C (long-term storage).
For routine on-site laboratory confirmation DNA extracts were subjected to IS2404 DRB PCR at KCCR and INH as previously described [6 (link), 10 (link), 35 (link)]. For comparative testing in the context of external quality assurance programs with conventional, gel-based IS2404 PCR (cPCR) [4 (link)–5 (link), 33 (link), 35 (link), 36 (link)] and a recently described modified IS2404 qPCR based on the assay published by Fyfe et al. [7 (link), 29 (link)] aliquots of DNA extracts were shipped to the Department of Infectious Diseases and Tropical Medicine (DITM), Munich, Germany by courier service at ambient temperature [10 (link)].
Beissner M., Phillips R.O., Battke F., Bauer M., Badziklou K., Sarfo F.S., Maman I., Rhomberg A., Piten E., Frimpong M., Huber K.L., Symank D., Jansson M., Wiedemann F.X., Banla Kere A., Herbinger K.H., Löscher T, & Bretzel G. (2015). Loop-Mediated Isothermal Amplification for Laboratory Confirmation of Buruli Ulcer Disease—Towards a Point-of-Care Test. PLoS Neglected Tropical Diseases, 9(11), e0004219.
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8

Genetic Variants in PTK7 and VANGL2

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DNA was extracted from newborn screening blood spots using the Gentra Puregene DNA Extraction Kit (Qiagen, Valencia, CA). The genomic structure of human PTK7 was determined using the NCBI GenBank (NT_007592.15, NM_001270398/ENST00000481273.5 and NP_001257327). The 20 exons of PTK7 were amplified by polymerase chain reactions (PCR) using primers flanking exon‐intron junctions. Primer sequences are available upon request. The PCR products were sequenced using the Prism Bigdye Terminator Kit (v3) on an ABI 3730XL DNA analyzer (Life Technologies, Carlsbad, CA). Both case and control samples were sequenced with either a specific forward or reverse primer. The detected variants were confirmed by repeating the PCR and re‐sequencing from both directions. VANGL2 was re‐sequenced in the 192 NTD cases following our previous publication (Lei et al., 2010). Sequencing results were analyzed using the Mutation Surveyor software V4.0.5 (Softgenetics, Stage College, PA).
Lei Y., Kim S., Chen Z., Cao X., Zhu H., Yang W., Shaw G.M., Zheng Y., Zhang T., Wang H, & Finnell R.H. (2019). Variants identified in PTK7 associated with neural tube defects. Molecular Genetics & Genomic Medicine, 7(4), e00584.
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9

Whole Exome Sequencing for DIPG and Pediatric Tumor Profiling

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For SU-DIPG samples and SF5609, genomic DNA was extracted from primary tissue using DNEasy Blood & Tissue kit (Qiagen #69504). Whole exome enrichment and library preparation was performed using 200 ng of genomic DNA and SureSelectXT Reagent Kit (Agilent #G9611A) with SureSelectXT Human All Exon v6 (Agilent #5190–8863) capture library. Libraries were sequenced on a NextSeq 500 by Stanford Functional Genomics Facility. All tumor-normal pairs were prepared and sequenced together. For CNMC samples, genomic DNA was extracted from frozen tissue using the Gentra Puregene DNA extraction kit according to the manufacturer’s instructions (Qiagen # 158667). For WES samples, Nextera Rapid Capture Exome kit (Illumina # 20020616) was used to prepare the paired-end libraries according to the manufacturer’s instructions using an average 36 ng of total starting genomic DNA. Sequencing was performed on Illumina HiSeq 2000 using rapid-run mode with 100 bp paired-end reads. WGS was performed using HiSeq X at 150bp read length.
Nagaraja S., Quezada M.A., Gillespie S.M., Arzt M., Lennon J.J., Woo P.J., Hovestadt V., Kambhampati M., Filbin M.G., Suva M.L., Nazarian J, & Monje M. (2019). Histone variant and cell context determine H3K27M reprogramming of the enhancer landscape and oncogenic state. Molecular cell, 76(6), 965-980.e12.
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10

Vector Copy Number Analysis

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Genomic DNA was prepared from spleen colonies or BM cells of transplanted mice sacrificed 24–28 weeks post-transplant using the Gentra Puregene DNA Extraction Kit (Qiagen, Valencia, CA). DNA (5 µg) was digested with EcoRI or BglII and Southern blot performed to identify presence of vector DNA or estimate VCN, respectively. A radiolabeled DNA probe was hybridized with the membrane and signal intensity of the band measured using a Molecular Dynamic Storm 860 Phosphoimager (Sunnyvale, CA) and its accompanying software.
Pestina T.I., Hargrove P.W., Zhao H., Mead P.E., Smeltzer M.P., Weiss M.J., Wilber A, & Persons D.A. (2015). Amelioration of murine sickle cell disease by nonablative conditioning and γ-globin gene-corrected bone marrow cells. Molecular Therapy. Methods & Clinical Development, 2, 15045-.
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