Raw whole genome sequencing data from mouse tumors was previously obtained28 (link). Briefly, three samples from each group (total of 12) were used, DNA from flash frozen extracted following manufacture’s protocol for Qiagen Genomic-tip 20/G kit. Sequencing was completed at a depth of 40 × with paired end, 150 base pair reads. DNA was prepared and sequenced using Illumina TruSeq Nano DNA library preparation and an Illumina HiSeq 2500. For this study, raw fastq files were assessed for quality control using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ) and trimmed using Trimmomatic41 (link). Files were aligned to mm10 mouse reference using BWA MEM42 with standard parameters. Picard tools (“Picard Toolkit.” 2019) was used to add read groups and remove duplicates. Samtools43 (link) was used to sort and index files.
Truseq nano dna library preparation
Manufactured by Illumina
Sourced in United States
The TruSeq Nano DNA Library Preparation kit is a tool designed for the construction of DNA libraries for next-generation sequencing. It provides a simple, streamlined workflow for preparing DNA samples for sequencing on Illumina platforms.
Automatically generated - may contain errors
Lab products found in correlation
Qiaamp dna mini kit, by Qiagen (2 mentions)
Truseq dna pcr free library preparation, by Illumina (2 mentions)
Hiseq x ten sequencer, by Illumina (2 mentions)
Hiseq x ten sequencing, by Illumina (2 mentions)
Hiseq 2500, by Illumina (1 mentions)
Genomic tip 20 g kit, by Qiagen (1 mentions)
Novaseq 6000, by Illumina (1 mentions)
Magattract hmw dna kit, by Qiagen (1 mentions)
Dneasy blood and tissue kit, by Qiagen (1 mentions)
6 protocols using truseq nano dna library preparation
1
Whole Genome Sequencing of Mouse Tumors
2
Multi-Platform Genomic Sequencing of Mollusk
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For the PacBio sequencing, the mantle tissue was sent to Brigham Young University (BYU, USA). High-molecular-weight DNA extraction was performed, and PacBio library construction was achieved following the single-molecule real-time (SMRT) bell construction protocol [29 ] . The library was sequenced using an SMRT cell of a PacBio Sequel II system v.9.0. The genomic DNA for short-read sequencing was extracted from the muscle tissue using the Qiagen MagAttract HMW DNA Kit, following the manufacturer’s instructions. The extracted DNA was sent to Macrogen Inc. for standard Illumina Truseq Nano DNA library preparation, and the WGS of 150 bp paired-end reads on the Illumina Novaseq 6,000 machine (Table 2 ).
3
DNA Extraction and Whole-Genome Sequencing Protocol
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
Sequencing of Cell Cycle Stages
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HCT116 were treated with MLN4924 for the indicated times and doses. Untreated G1 cells were isolated by elutriation at 750 × g, at 4 °C, at flow rate 15 ml/min. DNA from both G1 ( > 98% in G1 phase) and exponential growing (>50% cells in S phase) untreated cells as well as from re-replicating cells were extracted using the Qiagen DNeasy blood and tissue kit (cat# 69581). DNA samples were sequenced on HiSeq using Illumina TruSeq Nano DNA library preparation and paired-end sequencing. The mean coverage was at least 30X depth.
6
Genetic Basis of Xanthomonas Resistance
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A total of 7,484 F 2 individuals derived from Xtg-ART were established in the greenhouse, and leaves from each plant were harvested individually. Plants were allowed to grow back and were then inoculated with the highly pathogenic strain Xtg29 [4] .
Disease was monitored and scored on a scale from one to five at 14, 21, 28, and 49 days post inoculation, and the 750 most resistant individuals and the 761 most susceptible individuals were selected to form a resistant and susceptible pool, respectively. Both pools were randomly divided into three subpopulations of an equal number of samples. DNA was extracted from the previously harvested leaves and libraries for each subpopulation were prepared for whole genome sequencing using Illumina TruSeq Nano DNA Library Preparation, (Illumina, San Francisco, CA, USA). Libraries were then sequenced using 150 bp pairedend reads on a NovaSeq 6000 S4 flowcell. Reads were mapped on the genome sequence of M2289, the resistant parent of the Xtg-ART population [3] , and SNPs were determined using bcftools 'call' from a samtools 'mpileup' . After filtering for low (<50) and high (>400) read counts, and quality (>50 QUAL score), association between each SNP and resistance or susceptibility was tested by Cochran Mantel Haenszel test.
Disease was monitored and scored on a scale from one to five at 14, 21, 28, and 49 days post inoculation, and the 750 most resistant individuals and the 761 most susceptible individuals were selected to form a resistant and susceptible pool, respectively. Both pools were randomly divided into three subpopulations of an equal number of samples. DNA was extracted from the previously harvested leaves and libraries for each subpopulation were prepared for whole genome sequencing using Illumina TruSeq Nano DNA Library Preparation, (Illumina, San Francisco, CA, USA). Libraries were then sequenced using 150 bp pairedend reads on a NovaSeq 6000 S4 flowcell. Reads were mapped on the genome sequence of M2289, the resistant parent of the Xtg-ART population [3] , and SNPs were determined using bcftools 'call' from a samtools 'mpileup' . After filtering for low (<50) and high (>400) read counts, and quality (>50 QUAL score), association between each SNP and resistance or susceptibility was tested by Cochran Mantel Haenszel test.
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