Genomic dna buffer set

Manufactured by Qiagen

Sourced in Germany, United States, United Kingdom

The Genomic DNA Buffer Set is a collection of buffers designed for the extraction and purification of genomic DNA. The set includes buffers for cell lysis, DNA binding, washing, and elution, facilitating the efficient and reliable isolation of high-quality genomic DNA from a variety of sample types.

Automatically generated - may contain errors

Lab products found in correlation

Genomic tip 100 g, by Qiagen (13 mentions) Genomic tip, by Qiagen (6 mentions) Genomic tip 20 g, by Qiagen (5 mentions) Genomic tip 100 g kit, by Qiagen (5 mentions) Miseq platform, by Illumina (4 mentions) Genomic tip 100 g column, by Qiagen (4 mentions) Qubit dsdna hs assay kit, by Thermo Fisher Scientific (4 mentions) Primestar max premix, by Takara Bio (3 mentions) Qiaquick gel extraction kit, by Qiagen (3 mentions) Miseq instrument, by Illumina (3 mentions) Nextera xt dna library preparation kit, by Illumina (3 mentions) Rnase a, by Qiagen (3 mentions) Qubit 3.0 fluorometer, by Thermo Fisher Scientific (3 mentions) Plasmid midi kit, by Qiagen (3 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (3 mentions) Dna lobind tube, by Eppendorf (2 mentions) Genomic tip 500 g, by Qiagen (2 mentions) Genomic tip 20 g kit, by Qiagen (2 mentions) Qubit dsdna br assay kit, by Thermo Fisher Scientific (2 mentions) 100 g genomic tips, by Qiagen (2 mentions)

Close spelling variants of this product

DNA Buffer Set (9 citations) Genomic DNA buffer (6 citations) Genomic Buffer Set (5 citations)

54 protocols using genomic dna buffer set

Genomic DNA Extraction from Drechmeria flagrans

Check if the same lab product or an alternative is used in the 5 most similar protocols

For extraction of genomic DNA, D. flagrans was grown on CM-agar for 7 days. Spores were collected in 100 ml CM liquid medium and incubated at 28°C for 24 h at 180 rpm. Protoplasts were generated as described above and genomic DNA was extracted using Genomic DNA Buffer Set (Qiagen) and Genomic-tip 20/G (Qiagen) according to the manufacturer’s instruction. In total 12 μg of DNA were sent for sequencing.
The D. flagrans genome was sequenced using the PacBio RS technology (Pacific Biosciences, Menlo Park, CA, USA) with libraries prepared with the SMRTbell template prep kit 1.0 (Pacific Biosciences). The sequencing runs and assembly of the libraries were carried out by GATC biotech (Konstanz, Germany). The Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession SAEB00000000. The version described in this paper is version SAEB01000000. Raw reads were deposited at SRA under the accession SRR8400569.

Youssar L., Wernet V., Hensel N., Yu X., Hildebrand H.G., Schreckenberger B., Kriegler M., Hetzer B., Frankino P., Dillin A, & Fischer R. (2019). Intercellular communication is required for trap formation in the nematode-trapping fungus Duddingtonia flagrans. PLoS Genetics, 15(3), e1008029.

+ Open protocol

+ Expand

Genomic DNA Extraction and PCR Amplification of Photorhabdus rubra

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genomic DNA of P. rubra S4059 was extracted using the Genomic DNA buffer set (QIAGEN, 19060, Hilden, Germany), as mentioned above. All primers used in this study are listed in Table S6. All purified DNA fragments were amplified using PrimeSTAR^® Max Premix (TaKaRa, catalog number: R045A, Kusatsu, Japan). Blue TEMPase Hot Start Master Mix K (catalog number: 733-2584, Haasrode, Belgium) was used for homologous recombination event checking by PCR. All primers and plasmids were designed in A Plasmid Editor-ApE. The specificity of primers was checked by BLAST against the P. rubra S4059 genome. All primers were ordered from Integrated DNA technologies (Leuven, Belgium).

Wang X., Isbrandt T., Strube M.L., Paulsen S.S., Nielsen M.W., Buijs Y., Schoof E.M., Larsen T.O., Gram L, & Zhang S.D. (2021). Chitin Degradation Machinery and Secondary Metabolite Profiles in the Marine Bacterium Pseudoalteromonas rubra S4059. Marine Drugs, 19(2), 108.

+ Open protocol

+ Expand

Whole Genome Sequencing of E. coli Nissle 1917

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genomic DNA from 30 mL of overnight culture of control EcN was extracted using a Genomic DNA Buffer Set (19060, Qiagen) with the Qiagen protocol for Gram-negative bacteria (Qiagen Genomic DNA Handbook 06/2015) and the Genomic-tip 500/G (10262, Qiagen). Purified genomic DNA was sheared to a target fragment size of 10 kilobases using the Covaris g-TUBE™. All following steps were carried out in Eppendorf DNA LoBind tubes. Sheared DNA was repaired using the NEBNext FFPE Repair Mix (M6630), and repaired DNA purified from the reaction using Agencourt AMPure XP beads. DNA was then end-repaired and dA-tailed using the NEBNext End repair / dA-tailing Module (E7546) and again purified with AMPure XP beads. DNA was then prepared for MinION sequencing using the MinION Ligation Sequencing Kit 1D (SQK-LSK108). Briefly, adapters were ligated to the DNA using the MinION Adapter Mix (AMX1D) and NEB Blunt/TA Ligase Master Mix (M0367). Then the DNA product was purified using AMPure XP beads and the Minion Adapter Bead Binding Buffer (ABB). 350 ng of DNA product was then sequenced on a MinION R9.4 flow cell for 48 hours using the Running Buffer with Fuel Mix (RBF) and the Library Loading Bead Kit (EXP-LLB001). Average read lengths were 7 kilobases and the genome was sequenced with an average coverage of 50 reads.

Crook N., Ferreiro A., Gasparrini A.J., Pesesky M.W., Gibson M.K., Wang B., Sun X., Condiotte Z., Dobrowolski S., Peterson D, & Dantas G. (2019). Adaptive strategies of the candidate probiotic E. coli Nissle in the mammalian gut. Cell host & microbe, 25(4), 499-512.e8.

+ Open protocol

+ Expand

Efficient DNA Extraction from Swab and Lavage Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols

Each swab sample was extracted three times with 1 mL of PBS, and the combined mixture was centrifuged at 16,100g for 5 min. Similarly, each lavage sample was centrifuged at 16,100g for 5 min. The resulting pellets were used for further purification. The Genomic DNA Buffer Set (Qiagen, 19060) and Genomic-tip 20/G (Qiagen, 10223) were used for DNA purification. The pellets were resuspended in buffer B1 containing 20 µL of RNase A (10 mg/mL), followed by the addition of 20 µL of lysozyme (100 mg/mL) and 45 µL of proteinase K (20 mg/mL). The samples were incubated at 37 °C for 30 min, followed by the addition of 350 µL of buffer B2, gentle mixing, and incubation at 50 °C for 30 min. Thereafter, the manufacturer’s protocol was followed. The genomic DNA was eluted twice with 1 mL of buffer QF (pre-heated to 50 °C to increase yield). The eluted DNA was precipitated by the addition of 700 µL of isopropanol, followed by mixing and centrifugation at 12,000g at 4 °C for 15 min. The resulting DNA pellets were washed with 1 mL of cold 70% ethanol and again centrifuged at 12,000g at 4 °C for 10 min. The pellets were air-dried for 10 min and subsequently solubilized in 50 µL of TE.

Ho M., Moon D., Pires-Alves M., Thornton P.D., McFarlin B.L, & Wilson B.A. (2021). Recovery of microbial community profile information hidden in chimeric sequence reads. Computational and Structural Biotechnology Journal, 19, 5126-5139.

+ Open protocol

+ Expand

Genome Sequencing of Resp-Recombinant Lines

Check if the same lab product or an alternative is used in the 5 most similar protocols

A pool of 10 male pupae of lines L165 and L205 were homogenized in liquid nitrogen using mortar and pestle and DNA extractions were performed with QIAGEN Genomic-tip 100/G and the Genomic DNA Buffer Set (Qiagen, Hilden, Germany) according to the manufacturers’ instructions, but extending incubation times with buffer G2 containing proteinase K and RNase A to 12 h. HMW genomic DNA was sent to GATC Biotech for sequencing. Sequencing was done using an Illumina HiSeq2500 instrument, obtaining ~200 Mio paired end (2 × 150 bp) sequences per Resp-recombinant line. Shotgun genome assemblies were generated using the CLC Genomics Workbench v10.1. For PacBio sequencing, HMW genomic DNA was isolated from individual pupae of lines L165 and L205 by the Max Planck-Genome Centre Cologne (MPGCC) using the Qiagen MagAttract HMW DNA Kit. Sequencing of the size-selected HMW genomic DNA of each strain further purified with AMPure beads was performed at the MPGCC on a PacBio Sequel instrument. PacBio reads for both recombinant lines were assembled separately using the HGAP4 assembly pipeline implemented in the SMRT analysis software with standard settings. After genome sequencing of lines L165 and L205, primers were designed which amplified line-specific size polymorphisms and used to narrow down the breakpoint within all Resp-recombinant lines (Supplementary Methods, Supplementary Table 1).

Unbehend M., Kozak G.M., Koutroumpa F., Coates B.S., Dekker T., Groot A.T., Heckel D.G, & Dopman E.B. (2021). bric à brac controls sex pheromone choice by male European corn borer moths. Nature Communications, 12, 2818.

+ Open protocol

+ Expand

Genomic DNA Extraction from C. utilis

Check if the same lab product or an alternative is used in the 5 most similar protocols

C. utilis genomic DNA was extracted from growing cells by using the genomic DNA buffer set (Qiagen, Hilden, Germany) and Genomic-tip 100/G (Qiagen) according to the manufacturer’s instruction, and dissolved in 10 mM TE buffer (pH 8.0).

Yasukawa T., Oda A.H., Nakamura T., Masuo N., Tamura M., Yamasaki Y., Imura M., Yamada T, & Ohta K. (2022). TAQing2.0 for genome reorganization of asexual industrial yeasts by direct protein transfection. Communications Biology, 5, 144.

+ Open protocol

+ Expand

Long-Read Genome Sequencing of Microbial Species

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genomic DNA was extracted from a log-phase culture using QIAGEN Genomic-Tip 100/G and Genomic DNA Buffer Set as per manufacturer’s instructions. Nanodrop (Thermo Fisher Scientific, USA) was employed to assess DNA purity and Qubit (Thermo Fisher Scientific) was used to validate dsDNA content. DNA fragment size was checked by Pippin Pulse Electrophoresis (Sage Science, USA). A 15-20 Kb Genomic P6 Library was constructed for PacBio SMRT (Single Molecule Real-Time) sequencing (Ramaciotti Centre for Genomics, Sydney, Australia). Genome sequencing using PacBio RSII platform produced 657-Mb data (57,328 reads with the length of 1,000-50,923 bp, accession SRR10295884 in NCBI SRA database), representing approximately 170-fold coverage of the genome.

Zhu Y., Lu J., Zhao J., Zhang X., Yu H.H., Velkov T, & Li J. (2020). Complete genome sequence and genome-scale metabolic modelling of Acinetobacter baumannii type strain ATCC 19606. International journal of medical microbiology : IJMM, 310(3), 151412.

+ Open protocol

+ Expand

PacBio Sequencing of mcr-positive Strains

Check if the same lab product or an alternative is used in the 5 most similar protocols

Genomic DNA from mcr-positive strains were extracted for single-molecule real-time (SMRT) sequencing using the Blood and Cell Culture DNA Midi kit (Qiagen cat. no. 13343, CA) and Genomic DNA Buffer Set (Qiagen cat. no. 19060, CA), according to manufacturer’s protocols for preparation of Gram-negative bacteria sample and isolation of genomic DNA from bacteria. The 20-kb DNA libraries were prepared using the BluePippin size selection system following manufacturer’s instructions. High-throughput sequencing was performed on a PacBio RSII platform using the 360-min data collection protocol. The PacBio reads were assembled using the Hierarchical Genome Assembly Process 3 (HGAP3, SMRT Analysis v2.3.0). The completed genome sequences were submitted to NCBI Prokaryotic Genome Annotation Pipeline (PGAP) for annotation.

Wang Y., Hou N., Rasooly R., Gu Y, & He X. (2021). Prevalence and Genetic Analysis of Chromosomal mcr-3/7 in Aeromonas From U.S. Animal-Derived Samples. Frontiers in Microbiology, 12, 667406.

+ Open protocol

+ Expand

PacBio Sequencing and Genome Assembly of Xanthomonas

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Long read, SMRT sequencing (PacBio, Menlo Park, CA, United States) data were generated for five Xol strains and for the Xo strain X11-5A, to be used as an outgroup. DNA for SMRT sequencing was isolated by culturing strains on nutrient agar for 48 h then using the Genomic DNA buffer set and Genomic-tips according manufacturer instructions (Qiagen, Valencia, CA, United States). SMRT sequence was assembled using HGAP v4 (PacBio, Menlo Park, CA, United States). Genomes were circularized using circulator (Hunt et al., 2015 (link)). Assemblies and raw data have been deposited in NCBI (BioProject IDs PRJNA522807 and PRJNA522811; BioSample accessions SAMN03862116, SAMN02469650, SAMN10956066-68, SAMN10956070; raw sequencing files SRX5417793-98; Assembly accessions CP036251-56). Assembly CP036251 (X11-5A) replaces draft assembly GCF000212755.1 and assembly CP036253 (NCPPB4346) replaces draft assembly GCF001276975.1 (also in Bioproject PRJNA257008). Accessions for all genomes used in this study are listed in Supplementary Table S2.

Lang J.M., Pérez-Quintero A.L., Koebnik R., DuCharme E., Sarra S., Doucoure H., Keita I., Ziegle J., Jacobs J.M., Oliva R., Koita O., Szurek B., Verdier V, & Leach J.E. (2019). A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems. Frontiers in Plant Science, 10, 507.

+ Open protocol

+ Expand

Centipede DNA Extraction Protocol

Cited 1 time

Check if the same lab product or an alternative is used in the 5 most similar protocols

Adult centipedes were collected from the field at a stretch of shingle bank beach near Brora, northeastern Scotland (coordinates: 57°59'N, 03°55'W) as described previously [31 (link)]. Once returned to the lab, individual adults were sexed according to morphological criteria [8 (link), 32 ]. The final leg-bearing segment and the genital segments were removed by dissection from female adults. This was to ensure complete removal of the spermatheca from female specimens, to avoid any contamination with male DNA. Adults were snap frozen in liquid nitrogen and stored at -80°C until processing. Genomic DNA (gDNA) was extracted from male and female specimens with the Genomic DNA Buffer Set and Genomic-tip 20/G (Qiagen) according to the manufacturer’s instructions.

Green J.E., Dalíková M., Sahara K., Marec F, & Akam M. (2016). XX/XY System of Sex Determination in the Geophilomorph Centipede Strigamia maritima. PLoS ONE, 11(2), e0150292.

+ Open protocol

+ Expand

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!