DNA was extracted from prefrontal cortex where available (or generic cortex in a minority of cases) using lysis buffer from the QIAamp DNA Mini kit (Qiagen) followed by phenol chloroform extraction and isopropanol clean-up. Samples UMB4334, UMB4899, UMB4999, UMB5027, UMB5115, UMB5176, UMB5297, UMB5302, UMB1638, UMB4671, and UMB797 were processed at New York Genome Center using TruSeq Nano DNA library preparation (Illumina) followed by Illumina HiSeq X Ten sequencing to a minimum 200x depth. All remaining samples were processed at Macrogen using TruSeq DNA PCR-Free library preparation (Illumina) followed by minimum 30x sequencing of 7 libraries on the Illumina HiSeq X Ten sequencer, for a total minimum coverage of 210x per sample. All paired-end FASTQ files were aligned using BWA-MEM version 0.7.8 to the GRCh37 reference genome including the hs37d5 decoy sequence from Broad Institute63 .
Truseq dna pcr free library preparation
Manufactured by Illumina
Sourced in Japan
The TruSeq DNA PCR-Free library preparation kit is a lab equipment product from Illumina designed for DNA library preparation without the need for PCR amplification. It provides a streamlined workflow for generating high-quality DNA libraries from a variety of input sample types.
Automatically generated - may contain errors
Lab products found in correlation
Qiaamp dna mini kit, by Qiagen (3 mentions)
Truseq nano dna library preparation, by Illumina (2 mentions)
Hiseq x ten sequencing, by Illumina (2 mentions)
Hiseq x ten sequencer, by Illumina (2 mentions)
Mtdna extractor ct kit, by Fujifilm (1 mentions)
Mid output kit, by Illumina (1 mentions)
Hiseq x platform, by Illumina (1 mentions)
Miniseq platform, by Illumina (1 mentions)
Ampure xp bead, by Beckman Coulter (1 mentions)
Novaseq 6000, by Illumina (1 mentions)
Hiseq x ten, by Illumina (1 mentions)
5 protocols using truseq dna pcr free library preparation
1
DNA Extraction and Whole-Genome Sequencing Protocol
2
Mitochondrial DNA Extraction and Sequencing
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After treatment, genomic DNA of TK6 was extracted with the mtDNA extractor CT kit (WAKO, Osaka, Japan) and subjected to library preparation following the Illumina TruSeq DNA PCR-Free library preparation workflow with the prolonged ultrasonic shearing procedure to generate shorter double-stranded library fragments. Sequencing was performed on the Illumina HiSeqX platform at approximately 40 × sequencing depth with the read length of 2 × 150 bp. Genomic DNA from the control TK6 was further subjected to the enzymatic fragmentation and library preparation with the Lotus DNA Library Prep Kit (Integrated Device Technology, CA, USA). Modified fragmentation time and AMPure XP beads (Beckman Coulter, CA, USA) selection procedure were applied to generate shorter library fragments for sequencing. The constructed library was then sequenced on the Illumina MiniSeq platform with a Mid Output Kit (Illumina, CA, USA).
3
Whole-Genome Sequencing of Pooled Ileal Tumors
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Size-matched pooled ileal tumors (containing 9–12 tumors ≥2 mm in diameter) and mouse tails were used for genomic DNA extraction (n = 3 mice for Apc or Apc/Dok3). Genomic DNA was extracted using lysis buffer (10 mg/L Proteinase K, 0.1 mol/L Tris-HCl pH8.0, 0.4% SDS, 5 mmol/L EDTA, 0.2 mol/L NaCl) followed by phenol-chloroform extraction and isopropanol precipitation. Extracted genomic DNA was processed at Macrogen using Truseq DNA PCR-Free library preparation (Illumina). For whole-genome sequencing (WGS), tumor DNA samples were sequenced to an average depth of 100 × coverage, and matched non-tumor (tail) DNA samples were sequenced to an average depth of 30 × coverage, with 150 bp paired-end reads on Illumina Novaseq 6000 instruments. The Illumina platform generates raw images and base calling through an integrated primary analysis software called RTA (Real-Time Analysis). The BCL/cBCL (base calls) binary was converted into FASTQ using Illumina package bcl2fastq2-v2.20.0. The demultiplexing option (–barcode-mismatches) was set to perfect match (value: 0).
4
DNA Extraction and Whole-Genome Sequencing Protocol
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DNA was extracted from prefrontal cortex where available (or generic cortex in a minority of cases) using lysis buffer from the QIAamp DNA Mini kit (Qiagen) followed by phenol chloroform extraction and isopropanol clean-up. Samples UMB4334, UMB4899, UMB4999, UMB5027, UMB5115, UMB5176, UMB5297, UMB5302, UMB1638, UMB4671, and UMB797 were processed at New York Genome Center using TruSeq Nano DNA library preparation (Illumina) followed by Illumina HiSeq X Ten sequencing to a minimum 200x depth. All remaining samples were processed at Macrogen using TruSeq DNA PCR-Free library preparation (Illumina) followed by minimum 30x sequencing of 7 libraries on the Illumina HiSeq X Ten sequencer, for a total minimum coverage of 210x per sample. All paired-end FASTQ files were aligned using BWA-MEM version 0.7.8 to the GRCh37 reference genome including the hs37d5 decoy sequence from Broad Institute63 .
5
High-coverage brain tissue DNA sequencing
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Pulverized brain tissue was provided by Lieber Institute for Brain Development (Baltimore, MD). DNA was isolated from bulk brain tissue using lysis buffer from the QIAamp DNA Mini kit (Qiagen) followed by phenol chloroform extraction and isopropanol cleanup. DNA was then processed at Macrogen using the TruSeq DNA PCR-Free library preparation (Illumina) followed by a minimum of 30X sequencing of seven separate libraries on the Illumina HiSeq X Ten, for a total minimum coverage of 210×.
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