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Accel ngs methyl seq

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Accel-NGS Methyl-Seq is a library preparation kit designed for bisulfite sequencing of DNA methylation. The kit streamlines the conversion and library preparation process for whole-genome or targeted methylation analysis using next-generation sequencing (NGS) platforms.

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Lab products found in correlation

Ez dna methylation gold kit, by Zymo Research (3 mentions) M220 focused ultrasonicator, by Covaris (2 mentions) 2100 bioanalyzer, by Agilent Technologies (2 mentions) Novaseq 6000 system, by Illumina (2 mentions) Unmethylated λ phage dna, by Promega (2 mentions) Kapa hifi uracil dna polymerase, by Roche (1 mentions) Phusion u hot start dna polymerase, by Thermo Fisher Scientific (1 mentions) Allprep universal kit, by Qiagen (1 mentions) Bioruptor pico, by Diagenode (1 mentions) Nebnext ultra 2 library prep kit, by New England Biolabs (1 mentions)

Spelling variants of this product

Accel-NGS Methyl-Seq DNA Library Kit (68 citations) Accel-NGS Methyl-seq DNA Kit (5 citations) Accel-NGS Methyl-Seq DNA Library Preparation Kit (4 citations) Accel-NGS Methyl-Seq kit (4 citations) Accel-NGS Methyl-Seq DNA Library Kit with Unique Dual Indexing (2 citations) Accel-NGS Methyl-Seq DNA Library Kit - 24 rxns (2 citations) Accel-NGS Methyl-Seq Dual Indexing Kit - 96rxns (2 citations) Accel-NGS Methyl-Seq DNA Library prep kit (2 citations)

5 protocols using accel ngs methyl seq

1

Whole-Genome Bisulfite Sequencing in Aging Mice

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Whole-genome bisulfite sequencing was performed as previously described in Hadad et al.42 (link) in the hippocampi of 3- and 24-month-old animals. In this instance, bisulfite conversion and library construction were performed according to the manufacturer’s protocol (Accel-NGS Methyl-Seq, Swift Biosciences, Ann Arbor, MI). Libraries were sequenced (HiSeq 2500) to an average coverage depth of > 10× across the entire genome. Alignment and quantitation was as previously described by Hadad et al.42 (link) Quantitation at each CG and CH site covered at ≥10 × was then computed, and an average level of methylation across the genome for each mouse was calculated.
Unnikrishnan A., Hadad N., Masser D.R., Jackson J., Freeman W.M, & Richardson A. (2018). Revisiting the genomic hypomethylation hypothesis of aging. Annals of the New York Academy of Sciences, 1418(1), 69-79.
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2

Whole-Genome Bisulfite Sequencing of B-Cell Lines

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Human genomic DNA from lymphoblastoid B- cell lines was obtained from the Coriell Institute for Medical Research. Genomic DNA from the pre-B acute lymphoblastoid leukemia cell line REH (was isolated using the AllPrep Universal kit (Qiagen).
The EZ DNA Methylation Gold kit (Zymo Research) was used for sodium bisulfite conversion of DNA prior to library preparation. All WGBS libraries were prepared from 100 ng of genomic DNA. Accel-NGS Methyl-Seq (Swift BioSciences) and TruSeq DNA Methylation (Illumina Inc) were prepared according to the manufacturer’s protocols. SPLAT libraries were prepared as described previously [13 (link)] with the exception for libraries SPLAT-8 and SPLAT-9 which were amplified with the Phusion U Hot Start DNA polymerase (Thermo Fisher Scientific), whereas the other SPLAT libraries were amplified using the KAPA HiFi Uracil+ DNA polymerase (KAPA Biosystems).
Raine A., Liljedahl U, & Nordlund J. (2018). Data quality of whole genome bisulfite sequencing on Illumina platforms. PLoS ONE, 13(4), e0195972.
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3

Whole-Genome Bisulfite Sequencing of mCRPC Biopsies

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Fresh-frozen image-guided mCRPC biopsy samples were obtained as previously described17 (link). Benign-adjacent metastatic biopsies were identified for a subset of patients on centralized pathology review. DNA extraction was performed as previously described17 (link). WGBS libraries were prepared from 250 ng of genomic DNA with 0.5% un-methylated λ phage DNA (Promega) spiked in to measure bisulfite conversion efficiency. Bisulfite conversion efficiency was >99.5% in all samples, as measured by λ phage DNA spike-in. Samples were fragmented by Covaris M220 focused-ultrasonicator to an average size of 500 bp. Bisulfite conversion was performed using the EZ DNA methylation gold kit (Zymo Research). Library preparation was performed using Accel-NGS Methyl-Seq (Swift BioSciences). Library quality was monitored by 2100 Bioanalyzer (Agilent). Sequencing was performed at the UCSF Center for Advanced Technology sequencing core. 151bp paired end reads were sequenced on the Illumina Novaseq 6000 system.
Zhao S.G., Chen W.S., Li H., Foye A., Zhang M., Sjöström M., Aggarwal R., Playdle D., Liao A., Alumkal J.J., Das R., Chou J., Hua J.T., Barnard T.J., Bailey A.M., Chow E., Perry M., Dang H.X., Yang R., Moussavi-Baygi R., Zhang L., Alshalalfa M., Chang S.L., Houlahan K.E., Shiah Y.J., Beer T.M., Thomas G., Chi K.N., Gleave M., Zoubeidi A., Reiter R.E., Rettig M.B., Witte O., Kim M.Y., Fong L., Spratt D.E., Morgan T.M., Bose R., Huang F.W., Li H., Chesner L., Shenoy T., Goodarzi H., Asangani I.A., Sandhu S., Lang J.M., Mahajan N., Lara P.N., Evans C.P., Febbo P., Batzoglou S., Knudsen K.E., He H.H., Huang J., Zwart W., Costello J.F., Luo J., Tomlins S.A., Wyatt A.W., Dehm S.M., Ashworth A., Gilbert L.A., Boutros P.C., Farh K., Chinnaiyan A.M., Maher C.A., Small E.J., Quigley D.A, & Feng F.Y. (2020). DNA methylation landscapes in advanced prostate cancer. Nature genetics, 52(8), 778-789.
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4

Whole-Genome Bisulfite Sequencing of mCRPC Biopsies

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Fresh-frozen image-guided mCRPC biopsy samples were obtained as previously described17 (link). Benign-adjacent metastatic biopsies were identified for a subset of patients on centralized pathology review. DNA extraction was performed as previously described17 (link). WGBS libraries were prepared from 250 ng of genomic DNA with 0.5% un-methylated λ phage DNA (Promega) spiked in to measure bisulfite conversion efficiency. Bisulfite conversion efficiency was >99.5% in all samples, as measured by λ phage DNA spike-in. Samples were fragmented by Covaris M220 focused-ultrasonicator to an average size of 500 bp. Bisulfite conversion was performed using the EZ DNA methylation gold kit (Zymo Research). Library preparation was performed using Accel-NGS Methyl-Seq (Swift BioSciences). Library quality was monitored by 2100 Bioanalyzer (Agilent). Sequencing was performed at the UCSF Center for Advanced Technology sequencing core. 151bp paired end reads were sequenced on the Illumina Novaseq 6000 system.
Zhao S.G., Chen W.S., Li H., Foye A., Zhang M., Sjöström M., Aggarwal R., Playdle D., Liao A., Alumkal J.J., Das R., Chou J., Hua J.T., Barnard T.J., Bailey A.M., Chow E., Perry M., Dang H.X., Yang R., Moussavi-Baygi R., Zhang L., Alshalalfa M., Chang S.L., Houlahan K.E., Shiah Y.J., Beer T.M., Thomas G., Chi K.N., Gleave M., Zoubeidi A., Reiter R.E., Rettig M.B., Witte O., Kim M.Y., Fong L., Spratt D.E., Morgan T.M., Bose R., Huang F.W., Li H., Chesner L., Shenoy T., Goodarzi H., Asangani I.A., Sandhu S., Lang J.M., Mahajan N., Lara P.N., Evans C.P., Febbo P., Batzoglou S., Knudsen K.E., He H.H., Huang J., Zwart W., Costello J.F., Luo J., Tomlins S.A., Wyatt A.W., Dehm S.M., Ashworth A., Gilbert L.A., Boutros P.C., Farh K., Chinnaiyan A.M., Maher C.A., Small E.J., Quigley D.A, & Feng F.Y. (2020). DNA methylation landscapes in advanced prostate cancer. Nature genetics, 52(8), 778-789.
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5

Bisulfite Sequencing of CpG Methylation

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E. coli and reduced representation samples were assayed for CpG methylation content using bisulfite sequencing with the Illumina Miseq. 500 ng of E. coli DNA was sheared to 300bp using the Bioruptor Pico (Diagenode), then endrepaired and dAtailed using NEBNext Ultra II library prep kit (NEB). Methylated adapters (NEB) were ligated on using Blunt/TA ligase Master Mix, then libraries were bisulfite converted (Zymo MethylationLightning). Libraries were then amplified using indexed primers following NEB recommendations, but using Kapa Hifi Uracil as the polymerase. 10 ng of reduced representation samples MDAMB231 and MCF10A were prepared for Illumina sequencing using AccelNGS MethylSeq (Swift Biosciences). All samples were sequenced on an Illumina Miseq at JHU using v3 150 chemistry.
Simpson J.T., Workman R.E., Zuzarte P.C., David M., Dursi L.J, & Timp W. (2017). Detecting DNA cytosine methylation using nanopore sequencing. Nature methods, 14(4).
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