Project description:We report the methylome sequencing and annotation of Burkholderia pseudomallei D286 based on high-throughput profiling using PacBio SMRT technology
Project description:We report a new bisulfite-free 5mC and 5hmC base-resolution sequencing method: TET Assisted Pyridine borane Sequencing (TAPS). TAPS relies on mild reactions and detects DNA modifications directly, without affecting unmodified cytosines. We applied this method for the first time to whole genome sequencing in E14 mESC cell line. For comparsion we prepared whole-genome bisulfite sequencing in the same cell line. Compared with bisulfite sequencing, TAPS results in higher mapping rates, more even coverage and lower sequencing cost, enabling more informative and cheaper methylome analyses. We expect TAPS to become the new standard in epigenetic DNA sequencing.
2018-12-24 | GSE112520 | GEO
Project description:Neurospora species genome sequencing using PacBio long-read sequencing technology
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:We report a method for precisely stenciling the structure of individual chromatin fibers onto their composite DNA templates using non-specific DNA N6-adenine methyltransferases. Single-molecule long-read sequencing using PacBio of these chromatin stencils enables nucleotide-resolution readout of the primary architecture of multi-kilobase chromatin fibers (Fiber-seq).
Project description:Concurrent readout of sequence and base modifications from long unamplified DNA templates by PacBio single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000–50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.
Project description:Concurrent readout of sequence and base modifications from long unamplified DNA templates by PacBio single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000–50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.