DNA sequencing was performed using Illumina HiSeq 2500 Rapid Run at 150 cycles in paired-end mode. DNA concentration and quality was determined using the Qubit dsDNA HS kit (Invitrogen) and a Bioanalyzer 2100 (Agilent, Santa Clara, CA). DNA libraries were prepared using a KAPA High Throughput Library Preparation Kit with standard PCR library amplification (KAPA Biosystems, Wilmington, MA). TruSeq adapters (Illumina, San Diego, CA) with 6 bp indices were used to enable multiplexed sequencing. Illumina libraries were size selected using AMPure XP beads (Beckman Coulter, Indianapolis, IN). Library quality was measured on a Bioanalyzer 2100 by product size and concentration. On average, 43 million paired-end whole metagenome reads and 30 million paired-end VLP reads were generated for each sample. Sequencing reads were demultiplexed using the 6 bp TruSeq adapter sequences allowing for one mismatch using the Illumina CASAVA software. DNA quality control, HiSeq 2500 sequencing and library preparation was performed by the UT Southwestern Eugene McDermott Center for Human Growth and Development Next Generation Sequencing Core.
Standard pcr library amplification
Manufactured by Roche
The Standard PCR library amplification is a lab equipment used for the amplification of DNA libraries. It performs polymerase chain reaction (PCR) to generate multiple copies of target DNA sequences from a small initial amount. The core function of this equipment is to enable the exponential amplification of DNA samples.
Automatically generated - may contain errors
Lab products found in correlation
Kapa high throughput library preparation kit, by Roche (2 mentions)
Hiseq 2500 rapid run, by Illumina (2 mentions)
2100 bioanalyzer, by Agilent Technologies (2 mentions)
Truseq adapter, by Illumina (2 mentions)
Ampure xp bead, by Beckman Coulter (2 mentions)
Qubit dsdna hs kit, by Thermo Fisher Scientific (2 mentions)
Dneasy blood and tissue extraction kit, by Qiagen (1 mentions)
4 protocols using standard pcr library amplification
1
Whole Metagenome and VLP Sequencing
2
DNA Sequence Library Preparation
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Sequence libraries were created from enriched DNA using a 500 bp insert and standard PCR library amplification (KAPA Biosystems). Paired end sequences were obtained on either the Illumina Miseq or Nextseq platforms.
3
Bacterial Genome Sequencing from Colonies
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Isolates were grown on LB agar at 37°C for 24–48 hours and DNA was extracted from each isolate using the Qiagen DNeasy Blood and Tissue Extraction kit (Qiagen, Hilden, Germany) following the Gram-positive protocol with the addition of 1mg/ml of lysozyme and doubling the volumes. DNA was prepared for multiplexed, paired-end sequencing with a 500 base pair insert using Standard PCR Library Amplification (KAPA Biosystems, Woburn, MA). Genomes were sequenced on either a 2x100 bp paired-end HiSeq run or a 2x250 bp MiSeq run.
4
Whole Metagenome and VLP Sequencing
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DNA sequencing was performed using Illumina HiSeq 2500 Rapid Run at 150 cycles in paired-end mode. DNA concentration and quality was determined using the Qubit dsDNA HS kit (Invitrogen) and a Bioanalyzer 2100 (Agilent, Santa Clara, CA). DNA libraries were prepared using a KAPA High Throughput Library Preparation Kit with standard PCR library amplification (KAPA Biosystems, Wilmington, MA). TruSeq adapters (Illumina, San Diego, CA) with 6 bp indices were used to enable multiplexed sequencing. Illumina libraries were size selected using AMPure XP beads (Beckman Coulter, Indianapolis, IN). Library quality was measured on a Bioanalyzer 2100 by product size and concentration. On average, 43 million paired-end whole metagenome reads and 30 million paired-end VLP reads were generated for each sample. Sequencing reads were demultiplexed using the 6 bp TruSeq adapter sequences allowing for one mismatch using the Illumina CASAVA software. DNA quality control, HiSeq 2500 sequencing and library preparation was performed by the UT Southwestern Eugene McDermott Center for Human Growth and Development Next Generation Sequencing Core.
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