Truseq nano dna lt sample prep kit

Manufactured by Illumina

Sourced in United States

The TruSeq Nano DNA LT Sample Prep Kit is a laboratory equipment product designed for library preparation for next-generation sequencing. The kit provides reagents and protocols for fragmenting DNA samples and preparing sequencing libraries.

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Lab products found in correlation

Kapa library quantification kit, by Roche (2 mentions) 2100 bioanalyzer, by Agilent Technologies (2 mentions) Trizol reagent, by Thermo Fisher Scientific (2 mentions) Nanodrop 2000, by Thermo Fisher Scientific (2 mentions) Agencourt ampure beads, by Beckman Coulter (1 mentions) Hiseq 2500 platform, by Illumina (1 mentions) Bcl2fastq v1, by Illumina (1 mentions) Hiseq 2500 system, by Illumina (1 mentions) Agilent 2100 bioanalyzer, by Agilent Technologies (1 mentions) Hiseq 4000 platform, by Illumina (1 mentions) Hiseq 4000, by Illumina (1 mentions) Sonicator, by Covaris (1 mentions) Hiseq 2500, by Illumina (1 mentions) Smrtbell template prep kit 1, by Pacific Biosciences (1 mentions) Pacbio rs 2, by Pacific Biosciences (1 mentions) Nebnext ultra 2 rna library prep kit, by New England Biolabs (1 mentions) Zymo ez dna methylation lightning kit, by Zymo Research (1 mentions) Novaseq 6000 platform, by Illumina (1 mentions) Hiseq pe platform, by Illumina (1 mentions) Hiseq 2000, by Illumina (1 mentions)

Spelling variants of this product

TruSeq Nano kit (63 citations) TruSeq kits (44 citations) TruSeq Nano (27 citations) TruSeq Nano DNA (24 citations) LT Sample Prep Kit (12 citations) Illumina sample prep kit (8 citations) TruSeq Nano LT Kit (6 citations) TruSeq Nano Sample Prep kit (2 citations)

15 protocols using truseq nano dna lt sample prep kit

Comprehensive Microbiome Diversity Profiling

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DNA of the tissues and endophytes in the roots was extracted with the hexadecyl trimethyl ammonium bromide (CTAB) method (Li et al., 2017 (link)). DNA of the rhizosphere soil samples was extracted using a MoBio PowerSoil^® DNA Isolation Kit. The extracted DNA was detected by 1% agarose gel electrophoresis.
The 16S V4 and ITS1 region amplification of all samples was respectively performed by the universal primers 515F (5′-GTGCCAGCMGCCGCGGTAA-3′) - 806R (5′-GGACTACH VGGGTWTCTAAT-3′) and ITS1F (5′-CTTGGTCATTTAGAGGAAGTAA-3′) - ITS2 (5′- GCTGCGTTCTTCATCGATGC-3′) with the barcode on ABI GeneAmp^® 9700 PCR instrument (Caporaso et al., 2012 (link); Huang et al., 2015 (link)). After mixing and detecting with 2% agarose gel electrophoresis, the PCR products were recycled and purified with Agencourt AMPure Beads (Beckman Coulter, Indianapolis, IN). Finally, the PCR products were quantified using Quant-iT PicoGreen dsDNA Assay Kit and then mixed in proportion according to the concentration of each sample.
PCR amplicon libraries were generated by an Illumina TruSeq Nano DNA LT Sample Prep Kit (FC-121-4001). The library quality was then assessed and amplicon sequencing was performed on an Illumina HiSeq 2500 platform, generating 2 ×300 bp sequences. All raw data were submitted to the Sequence Read Archive (SRA) database with the accession numbers SRR7791517–SRR7791532.

Zhang X., Ye L., Kang Z., Zou J., Zhang X, & Li X. (2019). Mycorrhization of Quercus acutissima with Chinese black truffle significantly altered the host physiology and root-associated microbiomes. PeerJ, 7, e6421.

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sWGS Library Preparation and Sequencing

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Libraries for sWGS were prepared from 100ng DNA using modified TruSeq
Nano DNA LT Sample Prep Kit (Illumina) protocol41 (link). Quality and quantity of the libraries were assessed with
DNA-7500 kit on 2100 Bioanalyzer (Agilent Technologies) and with Kapa Library
Quantification kit (Kapa Biosystems) according to the manufacturer's
protocols. Sixteen to twenty barcoded libraries were pooled together in
equimolar amounts and each pool was sequenced on HiSeq4000 in SE-50bp mode.
Prior to sequencing we estimated the required sequencing depth by
adapting calculations made in previous work that explored the relationship
between sequencing depth (reads per sample) and copy number calling
accuracy42 (link). Based on these analyses,
we devised a power calculator for sWGS copy number analysis (see URL 1, described in 43 (link)). We estimated that with an average ploidy of 3 and
purity of 0.65, a sequencing depth of at least 2.7 million reads is required to
detect single, clonal copy-number changes (minimum 60kb) at 90% power and alpha
0.05. After analysis we determined that BritROC 3-star samples had an average
purity of 0.66, ploidy of 2.7, and were sequenced to an average depth of 8.6
million reads. This allowed us to detect single copy-number changes with 90%
power, and alpha 0.05 down to subclonal frequencies of 55%.

Macintyre G., Goranova T.E., De Silva D., Ennis D., Piskorz A.M., Eldridge M., Sie D., Lewsley L.A., Hanif A., Wilson C., Dowson S., Glasspool R.M., Lockley M., Brockbank E., Montes A., Walther A., Sundar S., Edmondson R., Hall G.D., Clamp A., Gourley C., Hall M., Fotopoulou C., Gabra H., Paul J., Supernat A., Millan D., Hoyle A., Bryson G., Nourse C., Mincarelli L., Navarro Sanchez L., Ylstra B., Jimenez-Linan M., Moore L., Hofmann O., Markowetz F., McNeish I.A, & Brenton J.D. (2018). Copy-number signatures and mutational processes in ovarian carcinoma. Nature genetics, 50(9), 1262-1270.

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Dwarf Minke Whale Skin DNA Sequencing

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Genomic DNA was extracted from approximately 0.05 g of the outer epidermal layer of the skin tissue of 11 dwarf minke whales using phenol–chloroform extraction. Extracted DNA was stored in TE buffer (10 mM Tris–HCl, 1 mM EDTA, pH 8.0).
DNA sequencing was performed by the Hokkaido System Science Co., Ltd (Sapporo, Japan). The DNA library was prepared with the TruSeq Nano DNA LT Sample Prep Kit (Illumina), following the manufacturer’s standard protocol. Extracted DNA was fragmented into c.a. 350 bps, and fragments with other sizes were removed using the provided sample purification beads. The adaptor sequences were ligated to each end of the fragments. The resulting DNA library was sequenced using paired-end 100-bp reads on one lane of Illumina HiSeq 2500 system (Illumina Inc. USA). Bcl2fastq v1.8.3 (Illumina, San Diego, CA) was used to demultiplex the data into individual samples based on the indexes used during the library preparation.

Malde K., Seliussen B.B., Quintela M., Dahle G., Besnier F., Skaug H.J., Øien N., Solvang H.K., Haug T., Skern-Mauritzen R., Kanda N., Pastene L.A., Jonassen I, & Glover K.A. (2017). Whole genome resequencing reveals diagnostic markers for investigating global migration and hybridization between minke whale species. BMC Genomics, 18, 76.

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sWGS Library Preparation and Sequencing

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Whole-Genome DNA Methylation Profiling of Wormwood Monoallergen Atopic Rhinitis

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Genomic DNA from peripheral blood mononuclear cell samples of wormwood monoallergen atopic rhinitis patients (n = 3) and healthy people (n = 3) during the pollen season was isolated using the DNA extraction kit (Omega, USA). We structured DNA libraries using the TruSeq Nano DNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) and used bisulfite to convert all unmethylated cytosine (C) in genomic DNA into uracil (U) using EpiTect® Fast Bisulfite (Qiagen, Germany) (the bisulfite conversion rate: 99%). The DNA library quality control was performed by using the Agilent 2100 Bioanalyzer (Agilent Technologies, California). The whole-genome DNA methylation was sequenced by using a Whole-Genome Shotgun (WGS) [48 (link)] with Illumina HiSeq (Illumina, San Diego, CA, USA). After clearing the linker sequence and low-quality reads, Bismark (0.19.0) [49 (link)] was used to align the reads to the genome (GRCh38/gh38) through Bowtie2(2.2.3) [50 (link)]; then, we identified base transversion events, classified, and counted them.

Guo X., Bai Y., Guo H., Wu P., Li H., Zhai L., Feng Y., Li J., Gao C, & Yun K. (2021). The Vista of Application of Specific Anaphylaxis Accurate Diagnosis Based on DNA Single-Nucleotide Methylation Sites. Contrast Media & Molecular Imaging, 2021, 8202068.

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Multiplex Illumina Library Preparation

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Single‐indexed Illumina libraries were prepared with the TruSeq Nano DNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) per the manufacturer's directions. The suggested 200 ng input of DNA was approximated by an input of PCR‐amplified DNA from each marker at the following amounts: Am12s at 31 ng, Ac12s at 37 ng, Ac16s at 34 ng, Ve16s at 34 ng, L2513/H2714 at 31 ng and L14735/H15149c at 37 ng, with the DNA from all six markers combined per sample to be individually indexed as one library and the total volume brought to 50 μL with the addition of resuspension buffer. A different amount of each amplicon was included in each library to account for anticipated PCR bias favouring shorter amplicons during the subsequent PCR enrichment step. Twelve individual libraries, one from each experimental treatment (4) and replicate (3), were pooled and submitted to the Notre Dame Genomics and Bioinformatics Core Facility (GBCF) for paired‐end sequencing on one MiSeq flowcell using a v3 600 cycle kit. Prior to sequencing, the GBCF checked library quality following MiSeq recommendations.

Evans N.T., Olds B.P., Renshaw M.A., Turner C.R., Li Y., Jerde C.L., Mahon A.R., Pfrender M.E., Lamberti G.A, & Lodge D.M. (2015). Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Molecular Ecology Resources, 16(1), 29-41.

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Genomic DNA Extraction and Sequencing of F2 Pumpkin Pools

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Total genomic DNA was extracted from fresh leaves of young seedlings using the CTAB method (VWI, China) as described in Liao et al. [41 (link)]. The F₂ offspring H-pool (hulled pumpkins) and HL-pool (hull-less pumpkins) were constructed by mixing 40 hulled and 40 hull-less F₂ individuals. A TruSeq Nano DNA LT Sample Prep Kit (Illumina, USA) was used to construct sequencing libraries. All libraries were sequenced on an Illumina HiSeq 4000 platform. The sequencing data quality was determined by FASTQC [55 (link)]. The QC standard pipelines were employed as described in Liao et al [41 (link)].

Lyu X., Shi L., Zhao M., Li Z., Liao N., Meng Y., Ma Y., Zhou Y., Xue Q., Hu Z., Yang J, & Zhang M. (2022). A natural mutation of the NST1 gene arrests secondary cell wall biosynthesis in the seed coat of a hull-less pumpkin accession. Horticulture Research, 9, uhac136.

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Shallow Sequencing for Copy Number Analysis

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The hybrid HSA3 and Neo3 cell lines were shallow sequenced to confirm copy number. Genomic DNA was prepared from cells and 500 ng DNA was fragmented using a Covaris sonicator. Genomic DNA libraries were prepared using Illumina TruSeq Nano DNA LT sample prep kit as per the manufacturer’s instructions and Illumina sequencing (50 bp, single-end reads) was performed on Illumina Hiseq 4000 (VUMC Cancer Centre, Amsterdam). FASTQ sequence files were obtained and reads were aligned to the human reference genome (hg19) using BWA and processed with Samtools v1.6^{85 (link)}. In R the BAM files were loaded into the Bioconductor package QDNAseq for copy number analysis. Human reference genome HG19 was used here as QDNAseq has pre-calculated bin annotations for genome build hg19. Sequence coverage was 0.23x coverage/base for HSA3 and 0.32x coverage/base for Neo3.

Naughton C., Huidobro C., Catacchio C.R., Buckle A., Grimes G.R., Nozawa R.S., Purgato S., Rocchi M, & Gilbert N. (2022). Human centromere repositioning activates transcription and opens chromatin fibre structure. Nature Communications, 13, 5609.

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Sequencing Haploid and Diploid Yeast Genomes

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Haploid YPH499 and S799 strains were sequenced using PacBio RS II (Pacific Biosciences) and MiSeq (Illumina, 2 × 300 bp; Illumina) systems. Cell-fusion diploid strains were sequenced using MiSeq (2 × 300 bp; Illumina). PacBio 20-kb SMRTbell libraries were generated by using the SMRTbell template prep kit 1.0 and BluePippin size selection systems (Pacific Biosciences) according to manufacturer instructions. The libraries were sequenced on three SMRT cells (one for YPH499 and two for S799). MiSeq libraries were generated using NEBNext Ultra DNA library prep kit for Illumina (E7370S; New England Biolabs, Ipswich, MA, USA) and the NEBNext multiplex oligonucleotides for Illumina (E7335S; New England Biolabs). Genome sequencing of TAQed plant genomes were examined by a commercial company (Hokkaido System Science) using an Illumina HiSeq 2500 (Illumina). Preparations for the genomic DNA library (350 bp inserts) were constructed using the TruSeq Nano DNA LT sample prep kit (Illumina) according to the manufacturer standard protocol.

Muramoto N., Oda A., Tanaka H., Nakamura T., Kugou K., Suda K., Kobayashi A., Yoneda S., Ikeuchi A., Sugimoto H., Kondo S., Ohto C., Shibata T., Mitsukawa N, & Ohta K. (2018). Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double-strand breaks. Nature Communications, 9, 1995.

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Multiomic Profiling of Plant Samples

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mRNA was extracted using TRIzol™ Reagent (Thermo Fisher). A total of 0.5 µg of total RNA per biological replicate were used for preparing 150 bp paired-end (PE) read libraries using the NEBNext® Ultra™ II RNA Library Prep Kit (New England Biolabs, Inc.). Small RNA was extracted using a Plant miRNA kit (Omega Bio-tek Inc.). One microgram of total RNA per biological replicate was employed for the construction of 50 bp single-end (SE) reads using NEBNext® Multiplex Small RNA Library Prep Set for Illumina™ (New England Biolabs, Inc.). Lastly, 2.5 µg of CTAB extracted-DNA per biological replicate were first treated with sodium-bisulfite using the Zymo EZ DNA Methylation-Lightning™ Kit (Zymo Research Corp.) and then built into 150 bp PE read libraries with the TruSeq Nano DNA LT Sample Prep Kit (Illumina Inc.) for whole-genome bisulfite sequencing (WGBS). All libraries were sequenced using an Illumina NovaSeq 6000 platform (Illumina Inc.). Read quality was evaluated with FastQC v.0.11.9 (Andrews. 2010 ) and multiqc v.1.9 (Ewels et al. 2016 (link)) for all sequencing types. Principal component analyses (PCA) were carried for all libraries per developmental stage using the plotPCA function from DESEQ2 for RNA data (Love et al. 2014 (link)) and the prcomp R function for WGBS libraries.

Orantes-Bonilla M., Wang H., Lee H.T., Golicz A.A., Hu D., Li W., Zou J, & Snowdon R.J. (2023). Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 136(5), 113.

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