Truseq methyl capture epic library prep kit

Manufactured by Illumina

Sourced in United States

The TruSeq Methyl Capture EPIC Library Prep Kit is a laboratory equipment product designed for DNA methylation analysis. It enables the preparation of libraries for whole-genome bisulfite sequencing (WGBS) on Illumina sequencing platforms.

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Lab products found in correlation

Xten platform, by Illumina (2 mentions) Agilent high sensitivity dna kit, by Agilent Technologies (2 mentions) Novaseq 6000, by Illumina (2 mentions) Hiseq 4000, by Illumina (2 mentions) S220 focused ultrasonicator, by Covaris (1 mentions) Nextseq 550 system, by Illumina (1 mentions) Wizard genomic dna purification kit, by Promega (1 mentions) Nextseq 550, by Illumina (1 mentions) Nebnext ultra rna library prep kit, by New England Biolabs (1 mentions) Small rna sample preparation kit, by Illumina (1 mentions) Qubit 4 fluorometer, by Thermo Fisher Scientific (1 mentions) Hiseq 2500 system, by Illumina (1 mentions) Ez dna methylation lightning kit, by Zymo Research (1 mentions) Hiseq 1500, by Illumina (1 mentions) Isolate 2 dna extraction kit, by Meridian Bioscience (1 mentions) Qiaamp dna mini kit, by Qiagen (1 mentions) Nextseq 500 system, by Illumina (1 mentions) Kapa library quant kit, by Roche (1 mentions) Hiseq x ten system, by Illumina (1 mentions) Qubit 2.0 fluorometer, by Thermo Fisher Scientific (1 mentions)

Spelling variants of this product

TruSeq kits (44 citations) TruSeq capture kit (5 citations) TruSeq Methyl Capture Epic kit (4 citations) TruSeq Methyl Capture EPIC LT Library Prep Kit (2 citations)

13 protocols using truseq methyl capture epic library prep kit

Targeted Bisulfite Sequencing for DNA Methylation

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HeLa cells were exposed to 200 µM SNOC and then incubated for the indicated times, or transduced with NOS2 for 48 h using Lipofectamine 3000. Subsequently, genomic DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega). Genomic DNA (1 µg) was fragmented to a peak size of 155–170 bp with a Covaris S220 focused ultrasonicator (Covaris, Inc., Woburn, MA, USA). Targeted bisulfite sequencing libraries were prepared using the TruSeq Methyl Capture EPIC Library Prep kit (Illumina) according to the manufacturer’s protocol, followed by 101 bp paired-end sequencing on a NextSeq550 system (Illumina). Analysis of methylation sites was performed using MethylSeq v2.0.0, which employed Bismark for methyl calling and aligned to the reference human genome (hg19) using Bowtie2. The ratio of the number of sequenced methylated cytosine reads to the total number of reads for each locus was evaluated. We only considered cytosine sites in targeted regions of Illumina-optimized capture probes with at least ≥10 reads and were measured in every sample. The sequence data files have been deposited in the DNA Data Bank of Japan (https://ddbj.nig.ac.jp/resource/sra-submission/DRA012330).

Okuda K., Nakahara K., Ito A., Iijima Y., Nomura R., Kumar A., Fujikawa K., Adachi K., Shimada Y., Fujio S., Yamamoto R., Takasugi N., Onuma K., Osaki M., Okada F., Ukegawa T., Takeuchi Y., Yasui N., Yamashita A., Marusawa H., Matsushita Y., Katagiri T., Shibata T., Uchida K., Niu S.Y., Lang N.B., Nakamura T., Zhang K.Y., Lipton S.A, & Uehara T. (2023). Pivotal role for S-nitrosylation of DNA methyltransferase 3B in epigenetic regulation of tumorigenesis. Nature Communications, 14, 621.

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Multimodal DNA Methylation Profiling of Solid Tumors

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Archival tissues from 133 FFPE primary lung adenocarcinomas, 39 lung squamous cell carcinomas, and 14 lung adenocarcinoma brain metastases were obtained from the Department of Pathology at UHN. We also obtained FFPE tissues from a cohort of 15 patients enrolled in the REACT study that included one bladder cancer, two cervical and endocervical cancers, six colorectal cancers, two lung adenocarcinomas, two melanomas, and two uterine corpus endometrial carcinomas. DNA methylation array analyses were performed at the Ontario Institute of Cancer Research as follows: 250 ng of DNA were treated using the Illumina FFPE DNA Restore Kit, hybridized to the Infinium EPIC methylation array, and scanned using an iScan instrument; raw data were processed using the Bioconductor package minfi v1.30 for normalization (Illumina method) and extraction of methylation values.
Methyl-seq analyses were also performed in parallel in the 15-patient cohort (REACT study) using a second aliquot of 500 ng of DNA from each sample; after bisulfite conversion, the DNA was subjected to library construction and targeted capture using the Illumina TruSeq Methyl Capture EPIC Library Prep Kit (targeting ~800,000 CpG sites), and followed by sequencing (Illumina NextSeq550, 70 million × 100 paired-end reads); methylation intensities were calculated with the Bismark v0.20.0 pipeline.

Xia D., Leon A.J., Cabanero M., Pugh T.J., Tsao M.S., Rath P., Siu L.L., Yu C., Bedard P.L., Shepherd F.A., Zadeh G., Chetty R, & Aldape K. (2020). Minimalist approaches to cancer tissue-of-origin classification by DNA methylation. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc, 33(10), 1874-1888.

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Identifying Differential Methylation Markers in Colorectal Cancer

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30 FF tissue samples of CRC (19 LNM+, 11 LNM-)were collected to identify differential methylation markers. Next, we independently constructed a genome-wide methylation library using TruSeq^® Methyl Capture EPIC Library Prep Kit (Illumina, USA, Catalog No. Fc-151-1002). After EPIC library was quality-assured with Agilent High-Sensitivity DNA Kit (Agilent, USA, Catalog No. 5067-4626), high-throughput sequencing was performed on Illumina X-TEN platform.

Yu Y., Xue W., Liu Z., Chen S., Wang J., Peng Q., Xu L., Liu X., Cui C, & Fan J.B. (2022). A novel DNA methylation marker to identify lymph node metastasis of colorectal cancer. Frontiers in Oncology, 12, 1000823.

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Comprehensive Genomic Analysis of Candidate Sex Genes

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Illumina sequencing experiments (Illumina NovaSeq 6000, Illumina, California) were performed at the levels of lncRNA, small RNA, and DNA methylation to quantify the digital expression and explore the gene regulation patterns of candidate sex genes. Libraries were constructed using a NEBNext Ultra RNA Library Prep Kit (Catalog No. E7530L, NEB) for mRNA, NEBNext Ultra RNA Library Prep Kit (NEB, Ispawich) for lncRNA, Small RNA Sample Preparation Kit (Catalog No. RS-200-0048, Illumina) for small RNA, and TruSeq Methyl Capture EPIC Library Prep Kit (Catalog No. FC-151-1002, Illumina) for DNA methylation, respectively, according to the manufacturers’ instructions.
In the analysis of RNA-seq, lncRNA-seq, and small RNA (sRNA)-seq data, rRNA/tRNA contaminants were removed by mapping the reads to rRNA/tRNA sequences from public databases. Transcripts of lncRNAs were assembled using Trinity V2.6.6 with the parameter settings for strand-specific reads (“--SS_lib_type RF”). The obtained sequences were used to search the National Center for Biotechnology Information (NCBI) RefSeq non-redundant proteins (NR) database. Small RNA reads and bisulfite sequencing reads were mapped to the reference genome using Bowtie2 v2.3.4.1 and Bismark v0.16.3 [96] (link), respectively. The alignment results were visualized using Integrative Genomics Viewer (IGV) v2.4.14 [97] (link).

Xia Z., Dai X., Fan W., Liu C., Zhang M., Bian P., Zhou Y., Li L., Zhu B., Liu S., Li Z., Wang X., Yu M., Xiang Z., Jiang Y, & Zhao A. (2022). Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants. Genomics, Proteomics & Bioinformatics, 20(6), 1119-1137.

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Reduced-representation bisulfite sequencing of pancreatic cells

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Genomic DNA was extracted from pellets of freshly sorted and cultured pancreatic acinar and ductal cells using the Zymo Quick-DNA^TM MiniPrep kit (Zymo Research, Irvine, CA, D3024) as according to manufacturer instructions. DNA quality was verified by Qubit 4 Fluorometer (Thermo Fisher Scientific). Library preparation was performed on 500–1000 ng of genomic DNA using the TruSeq Methyl Capture EPIC Library Prep Kit (Illumina, San Diego, CA, FC-151-1003), with which bisulfite conversion and PCR amplification of regions of interest was performed. Sequencing of the resulting reduced-representation DNA methylation sequencing libraries was performed using an Illumina NovaSeq 6000 at the GCCRI Genome Sequencing Facility. Alignment of sequencing files to GRCh38 and CpG calling was performed using Bismark 0.19.1. For subsequent analysis, only CpG sites for which there were at least 10 aligned reads for all samples were used. Methylation at a CpG site was calculated as the number of methylated reads divided by the total number of reads at that site (β-value), and the methylation of a genomic region was calculated as the mean of the β-values of all sites within that region. Differential methylation between regions was calculated using two-tailed Student’s t test, with a region being considered differentially methylated if the FDR corrected p value was less than 0.05.

Xu Y., Nipper M.H., Dominguez A.A., Ye Z., Akanuma N., Lopez K., Deng J.J., Arenas D., Sanchez A., Sharkey F.E., Court C.M., Singhi A.D., Wang H., Fernandez-Zapico M.E., Sun L.Z., Zheng S., Chen Y., Liu J, & Wang P. (2024). Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset. Nature Communications, 15, 818.

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Profiling Methylation in Pediatric Brain Tumors

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Genomic DNA was extracted from frozen sections of xenografts derived from the quadruple-mutant (i.e., DKO-G34R-MYCN) vFNPCs. hESC-derived vFNPCs were used as a control cell type. To minimize contamination of murine cells, all sections were stained with H&E and tumor parts were micro-dissected. After the quality control process, a sequencing library was created from the genomic DNA using TruSeq Methyl Capture EPIC Library Prep Kit (Illumina) and sequenced by Illumina HiSeq4000. Sequencing data were mapped to the human genome (hg38) using Map with BWA on the galaxy website (https://usegalaxy.org). DNA methylation data of patient tumors were obtained from GSE36278 (Sturm et al., 2012 (link)).

Funato K., Smith R.C., Saito Y, & Tabar V. (2021). Dissecting impact of regional identity and oncogenic role of human-specific NOTCH2NL in an hESC model of H3.3G34R mutant glioma. Cell stem cell, 28(5), 894-905.e7.

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Targeted Bisulfite Sequencing for 5hmC Profiling

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To validate our results and to establish the feasibility of using next generation sequencing (NGS) to profile 5hmC in lung tissues, the total methylation profiling was repeated among 5 pairs of tumor and adjacent normal tissues using the targeted bisulfite sequencing (Methyl-Seq). Briefly, 1000 ng of gDNA was sheared to yield fragment DNA between 100–300 base pair. These fragment DNA was further end-repaired, 3′-end adenylated, ligated, and hybridized; and captured DNA was bisulfite-converted using the Illumina TruSeq Methyl Capture EPIC Library Prep Kit (Illumina, Inc., San Diego, CA) [32] . Last, DNA was PCR-amplified and sequenced on Illumina Hi-Seq2500 System.

Wang Z., Du M., Yuan Q., Guo Y., Hutchinson J.N., Su L., Zheng Y., Wang J., Mucci L.A., Lin X., Hou L, & Christiani D.C. (2020). Epigenomic analysis of 5-hydroxymethylcytosine (5hmC) reveals novel DNA methylation markers for lung cancers. Neoplasia (New York, N.Y.), 22(3), 154-161.

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Targeted DNA Methylation at SHB Locus

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HeLa cells were transfected with pEF1a-GFP-Puro and pEF1a-mCherry for control baseline or pGK-dCas9-Suntag-tagBFP2, pEF1a-mCherry-SHB1 sgRNA, and pEF1a-αGCN4-DNMT3A for targeted methylation at SHB locus in triplicate. Transfected cells were sorted for GFP and mCherry positive (control baseline) or GFP, mCherry and BFP positive (targeted methylation at SHB locus) and subjected to DNA extraction using the ISOLATE II DNA extraction kit (Bioline, catalog no. BIO-52067). We used 250 ng of genomic DNA from each replicate for library preparation and subsequently pooled for target enrichment using the TruSeq methyl capture EPIC library prep kit (Illumina, catalog no. FC-151-1002) following manufacturer's instructions. Libraries were bisulfite converted using EZ DNA methylation Lightning kit (Zymo Research, D5030) and amplified for 10 cycles. Single-end 100 bp sequencing was performed on an Illumina HiSeq 1500.

Pflueger C., Tan D., Swain T., Nguyen T., Pflueger J., Nefzger C., Polo J.M., Ford E, & Lister R. (2018). A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs. Genome Research, 28(8), 1193-1206.

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Bisulfite Sequencing of CpG Islands

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CpG region capture and bisulphite converted 100 bp paired end sequencing was carried out on 500 ng DNA using the Illumina Tru-seq Methyl Capture Epic Library Prep kit (cat. FC-151-1003) on the Illumina HiSeq-4000. Adaptors sequences were removed using Cutadapt (version 1.11), aligned to GRCh37 using bwa-meth (version 0.2.0) and duplicate alignments were marked using Picard (version 1.129). Methylation at 865,859 known CpGs from the Illumina Epic assay were counted using the qbasepileup tool (https://github.com/AdamaJava/adamajava), using non-duplicate reads with MAPQ quality over 10 that passed vendor quality testing and with a minimum of 10 reads. CpG positions reported as having poor accuracy on the epic array [40 (link)] were removed. Methylation value was scored as a β value ratio, ranging from 0 (fully unmethylated) to 1 (fully methylated). Quantile normalisation was carried out on beta values using the R package preprocessCore to control for technical variation and aid comparison across different samples. Further filtering removed any CpG position where two or more samples had low coverage and replaced a low coverage position from a single sample with the median value of the other CpG methylation. The top 1000 most variable probes across the clone samples were selected and used with dist (Euclidean) and hclust (complete) R functions for hierarchical clustering.

Akgül S., Patch A.M., D’Souza R.C., Mukhopadhyay P., Nones K., Kempe S., Kazakoff S.H., Jeffree R.L., Stringer B.W., Pearson J.V., Waddell N, & Day B.W. (2019). Intratumoural Heterogeneity Underlies Distinct Therapy Responses and Treatment Resistance in Glioblastoma. Cancers, 11(2), 190.

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DNA Extraction and NGS Library Preparation

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DNA from PBMCs (n = 4) was extracted using QIAamp DNA Mini kit according to the manufacturer’s protocol (QIAGEN). The NGS library preparation and sequencing was conducted as follows in the Institute of Genomics Core Facility, University of Tartu. Libraries were prepared with TruSeq Methyl Capture EPIC Library Prep kit (Illumina Inc.; San Diego, California, USA), according to manufacturer's instructions and quantified using Illumina-specific KAPA Library Quant Kit (Kapa Biosystems, Wilmington, MA, USA). Sequencing was carried out on an Illumina NextSeq500 System in paired end 2 × 100 bp mode. Sequencing data were demultiplexed using the Illumina Local Run Manager Generate FASTQ Analysis Module v2.0.

Anier K., Somelar K., Jaako K., Alttoa M., Sikk K., Kokassaar R., Kisand K, & Kalda A. (2022). Psychostimulant-induced aberrant DNA methylation in an in vitro model of human peripheral blood mononuclear cells. Clinical Epigenetics, 14, 89.

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