DNA from fecal pellets was extracted with DNeasy Power Soil Pro kit (Qiagen) following manufacturer’s protocol. DNA quality control was performed with the Agilent 4,200 Tape Station system using the Genomic DNA ScreenTape analysis kit (Agilent, Santa Clara, CA, United States), only DNAs having a DIN > 6.5 were used for library preparation.
Genomic dna screentape analysis kit
Manufactured by Agilent Technologies
Sourced in United States
The Genomic DNA ScreenTape Analysis kit is a laboratory instrument used for the automated analysis of genomic DNA samples. It provides a rapid and efficient way to assess the size, concentration, and quality of genomic DNA samples.
Automatically generated - may contain errors
Lab products found in correlation
4150 tapestation system, by Agilent Technologies (2 mentions)
Qubit 3.0 fluorometric quantitation dsdna high sensitivity kit, by Thermo Fisher Scientific (2 mentions)
Ampure xp bead, by Beckman Coulter (2 mentions)
Dneasy powersoil pro kit, by Qiagen (1 mentions)
4200 tapestation system, by Agilent Technologies (1 mentions)
Nextseq 500, by Illumina (1 mentions)
2200 tapestation system, by Agilent Technologies (1 mentions)
Trueseq exome kit, by Illumina (1 mentions)
Trueseq rapid exome kit, by Illumina (1 mentions)
4 protocols using genomic dna screentape analysis kit
1
Fecal DNA Extraction for Metagenomic Analysis
2
Microbial Mat DNA Extraction and Sequencing
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Microbial mat plugs were extracted from Mushroom Spring, Yellowstone National Park, USA on July 30, 2009 across a series of temperatures: 50°C, 55°C, 60°C, 65°C. DNA was quantified using the Qubit 3.0 Fluorometric Quantitation dsDNA High Sensitivity kit (ThermoFisher Scientific, Waltham, MA, USA) and stored for future use at -80°C. DNA extractions were analyzed using the Genomic DNA ScreenTape Analysis kit on the 4150 TapeStation System (both from Agilent, Santa Clara, CA, USA). Size selection using AMPure XP beads (Beckman Coulter, San Jose, CA, USA) increased DNA fragment length from a mean of 2 kb up to 6 kb with high recovery of DNA. Size selected DNA was prepped for sequencing using the Oxford Nanopore Technologies (ONT) 1D Genomic DNA by Ligation library preparation kit (SQK-LSK109, Oxford Nanopore Technologies, Oxford, UK). Libraries were then sequenced using the ONT MinION sequencer using one FLO-MIN106D R9 Version Rev D flow cell per temperature sample. Sequencing was run on a MacBook Pro (model A1502, Apple) using ONT's MinKNOW software. Automatic basecalling through this software was turned off. Sequencing runs lasted between 24 and 44 hours. Basecalling was completed using the ONT software Guppy (https://github.com/nanoporetech/pyguppyclient.git) with default parameters.
3
Metagenomic Sequencing of Thermophilic Microbial Mats
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Microbial mat plugs were extracted from Mushroom Spring, Yellowstone National Park, USA on July 30, 2009 across a series of temperatures: 50°C, 55°C, 60°C, 65°C. DNA was quantified using the Qubit 3.0 Fluorometric Quantitation dsDNA High Sensitivity kit (ThermoFisher Scientific, Waltham, MA, USA) and stored for future use at −80°C. DNA extractions were analyzed using the Genomic DNA ScreenTape Analysis kit on the 4150 TapeStation System (both from Agilent, Santa Clara, CA, USA). Size selection using AMPure XP beads (Beckman Coulter, San Jose, CA, USA) increased DNA fragment length from a mean of 2kb up to 6kb with high recovery of DNA. Size selected DNA was prepped for sequencing using the Oxford Nanopore Technologies (ONT) 1D Genomic DNA by Ligation library preparation kit (SQK-LSK109, Oxford Nanopore Technologies, Oxford, UK). Libraries were then sequenced using the ONT MinION sequencer using one FLO-MIN106D R9 Version Rev D flow cell per temperature sample. Sequencing was run on a MacBook Pro (model A1502, Apple) using ONT’s MinKNOW software. Automatic basecalling through this software was turned off. Sequencing runs lasted between 24–44 hours. Basecalling was completed using the ONT software Guppy (https://github.com/nanoporetech/pyguppyclient.git ) with default parameters.
4
Next-Generation Sequencing Protocol for Exome Analysis
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Libraries for NGS were produced from Illumina Nextera exome sequencing kits (Illumina). DNA obtained from formalin‐fixed right ventricle was processed using TrueSeq Exome kit (Illumina, San Diego, CA, USA), and lymphocyte‐derived DNA using TrueSeq Rapid Exome kit (Illumina) according to the manufacturer’s instructions. Quantification for NGS was carried out using the Genomic DNA ScreenTape Analysis kit.
tape station analysis was used (2200 tape station system, software version 8.4.1, Agilent). An Illumina NextSeq 500 (Illumina) with equal loading of library preparation was used to collect 80 million paired end reads, 75‐bases in length, divided across four flow cells. Following sequencing, several global analyses were reported by the Illumina platform, including number of reads, read depth and GC content profiles.
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