Log In Sign up
The largest database of trusted experimental protocols

Genomic tip protocol

Manufactured by Qiagen
Visit Supplier
Sourced in United States

The Genomic Tip protocol is a laboratory procedure used for the purification and concentration of genomic DNA from a variety of sample types. It employs a silica-based membrane technology to efficiently capture and elute high-quality genomic DNA.

Automatically generated - may contain errors

Lab products found in correlation

Genomic tip kit, by Qiagen (2 mentions) Hiseq 2500 rapid flow cell, by Illumina (2 mentions) Sqk lsk109 kit, by Oxford Nanopore (1 mentions) Qubit 2.0 fluorimeter, by Thermo Fisher Scientific (1 mentions) Dna clean concentrator 5 column, by Zymo Research (1 mentions) G tube, by Covaris (1 mentions)

Close spelling variants of this product

Genomic-tip

3 protocols using genomic tip protocol

1

Hydroponic High-Molecular-Weight DNA Extraction and Nanopore Sequencing

Check if the same lab product or an alternative is used in the 5 most similar protocols
The Golden variety of A. hortensis was grown hydroponically in a growth chamber at BYU as previously described. Plants were dark-treated for 72 h at which point young leaf tissue was harvested and extracted for high molecular weight (HMW) genomic DNA using the Qiagen (Germantown, MD) Genomic-tip protocol. The DNA concentration was checked using the dsDNA High Sensitivity DNA Assay on the Qubit® 2.0 Fluorimeter (Invitrogen, Merelbeke, Belgium).
Samples for DNA sequencing were prepared with and without fragmentation using Covaris g-TUBEs (Woburn, MA) and the ZYMO DNA Clean & Concentrator-5 column (Irvine, CA, United States). Samples were fragmented using both the ZYMO DNA kit and Covaris g-TUBEs following manufacturer’s instructions. Samples prepared with the Covaris g-TUBEs were fragmented at several centrifugation speeds, including 3,800, 4,000, and 4,200 RPM. In total, nine libraries from the original DNA stock were prepared for sequencing using the 1D Genomic DNA by Ligation MinION library preparation kit. Libraries were sequenced on R9 flow cells on a MinION for 48 h using MinKNOW 2.0 software with the following settings: DNA, PCR-free, no multiplexing, SQK-LSK109 kit (Oxford Nanopore Technologies, Ltd., Oxford, United Kingdom). No alterations were made to voltage or time. Albacore v2.3.1, part of the MinKNOW package, was used for base calling.
Hunt S.P., Jarvis D.E., Larsen D.J., Mosyakin S.L., Kolano B.A., Jackson E.W., Martin S.L., Jellen E.N, & Maughan P.J. (2020). A Chromosome-Scale Assembly of the Garden Orach (Atriplex hortensis L.) Genome Using Oxford Nanopore Sequencing. Frontiers in Plant Science, 11, 624.
+ Open protocol
+ Expand
2

Metagenomic DNA Extraction from Sponge Samples

Check if the same lab product or an alternative is used in the 5 most similar protocols
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.
+ Open protocol
+ Expand
3

Metagenomic DNA Extraction from Sponge Samples

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

Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required

Sign up now

Revolutionizing how scientists
search and build protocols!