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Improved tagmentation-based whole genome bisulfite sequencing for input DNA from less than 100 cells

ABSTRACT: We improved the tagmentation-based whole genome bisulfite sequencing technology, enabling stable library construction with complexity from minimally 0.5ng of initial genomic DNA, which equals less than 100 cells. This new approach is highly attractive for the complete methylome analysis of very limited cell numbers, e.g., pre-implantation embryos, or tiny biopsy specimens.

ORGANISM(S): Oryza sativa

PROVIDER: GSE57062 | GEO | 2014/05/01

SECONDARY ACCESSION(S): PRJNA245358

REPOSITORIES: GEO

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Improved tagmentation-based whole genome bisulfite sequencing for input DNA from less than 100 cells

Project description:We improved the tagmentation-based whole genome bisulfite sequencing technology, enabling stable library construction with complexity from minimally 0.5ng of initial genomic DNA, which equals less than 100 cells. This new approach is highly attractive for the complete methylome analysis of very limited cell numbers, e.g., pre-implantation embryos, or tiny biopsy specimens. Applying this newly modified T-WGBS, we sequenced the methylome of a rice strain using libraries constructed from 10 ng, 1 ng and 0.5 ng of input genomic DNA. Two libraries were independently constructed and sequenced for each aliquot of input genomic DNA

2014-05-01 | E-GEOD-57062 | biostudies-arrayexpress

Multiplexed and ultralow-input ChIP-seq enabled by tagmentation-based indexing and facile microfluidics

Project description:Epigenome constitutes an important layer that regulates gene expression and dynamics during development and diseases. Extensive efforts have been made to develop epigenome profiling methods using a low number of cells and with high throughput. Chromatin immunoprecipitation (ChIP) is the most important approach for profiling genome-wide epigenetic changes such as histone modifications. In this report, we demonstrate microfluidic ChIPmentation (mu-CM), a microfluidic technology that enables profiling cell samples that individually do not generate enough ChIP DNA for sequencing library preparation. We used a simple microfluidic device to allow 8 samples to be processed simultaneously. The samples were indexed differently using a tagmentation-based approach (ChIPmentation) and then merged for library preparation. Histone modification profile for each individual sample was obtained by demultiplexing the sequencing reads based on the indexes. Our technology allowed profiling 20 cells and is well suited for cell-type-specific studies using low-abundance tissues.

2020-09-22 | GSE152233 | GEO

Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing.

Project description: Not available

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Transposase assisted tagmentation of RNA/DNA hybrid duplexes

Project description:Tn5-mediated transposition of double-strand DNA has been widely utilized in various high-throughput sequencing applications. Here, we report that the Tn5 transposase is also capable of direct tagmentation of RNA/DNA hybrids in vitro. As a proof-of-concept application, we utilized this activity to replace the traditional library construction procedure of RNA sequencing, which contains many laborious and time-consuming processes. Results of Transposase assisted RNA/DNA hybrids Co-tagmEntation (termed “TRACE-seq”) are comparable to traditional RNA-seq methods in terms of detected gene number, gene body coverage, gene expression measurement, library complexity, and differential expression analysis; at the meantime, TRACE-seq enables a one-tube library construction protocol and hence is more rapid (within 6h) and convenient. We expect this tagmentation activity on RNA/DNA hybrids to have broad potentials on RNA biology and chromatin research.

2020-07-29 | GSE143422 | GEO

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

Project description:Massively parallel DNA sequencing of thousands of samples in a single machine-run is now possible, but the preparation of the individual sequencing libraries is expensive and time-consuming. Tagmentation-based library construction, using the Tn5 transposase, is efficient for generating sequencing libraries but currently relies on undisclosed reagents, which severely limits development of novel applications and the execution of large scale projects. Here, we present simple and robust procedures for Tn5 transposase production and optimized reaction conditions for tagmentation-based sequencing library construction. We further show how molecular crowding agents both modulate library lengths and enable efficient tagmentation from sub-picogram amounts of cDNA. Comparison of single-cell RNA-sequencing libraries generated using produced and commercial Tn5 demonstrated equal performances in terms of gene detection and library characteristics. Finally, as naked Tn5 can be annealed to any oligonucleotide of choice, for example molecular barcodes in single-cell assays or methylated oligonucleotides for bisulfite sequencing, custom Tn5 production and tagmentation enables innovation in sequencing-based applications.

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Tagmentation (CUT&Tag) assay for ATF4 in HCT116 (Human colorectal cancer) cells

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Transposase assisted tagmentation of RNA/DNA hybrid duplexes

Project description:Transposase assisted tagmentation of RNA/DNA hybrid duplexes

| PRJNA600433 | ENA

Multiplexed and ultralow-input ChIP-seq enabled by tagmentation-based indexing and facile microfluidics

Project description:Multiplexed and ultralow-input ChIP-seq enabled by tagmentation-based indexing and facile microfluidics

| PRJNA638667 | ENA

Tagmentation-based Whole Genome Bisulfite Sequencing

Project description:We demonstrated the reliability of the tagmentation-based whole genome bisulfite sequencing in direct comparison with the conventional whole genome bisulfite sequencing.

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Allele-specific binding analysis of rs242561 by NRF2 ChIP tagmentation sequencing

Project description:We identified a SNP rs242561, located within a regulatory region of the MAPT gene (encoding microtubule-associated protein Tau). It was consistently occupied by NRF2/sMAF in multiple ChIP-seq experiments, and its strong-binding allele increased transactivation, and accorded higher mRNA levels in cell lines and human brain. To confirm the allele-specific binding, we conducted ChIP tagmentaion sequencing experiment in human lymphoblastoid cell line GM12763 which is heterozygous for rs242561. NRF2 ChIP DNA was isolated from GM12763 cells treated with Sulforaphane (SFN) in triplicates. The region containing rs242561 was amplified using primers, Fwd 5â??-AGCCTTCCCTGTCCTTGATT-3â??, Rev 5â??-GGACCGAGCTTCCAGTCTAA-3â??, and tagmentated using Tn5-based transposition for library construction. Libraries were sequenced on Illumina MiSeq. NRF2 ChIP tagmentation sequencing of a 241bp intron region in MAPT gene using GM12763 treated with sulforaphane

2016-04-14 | E-GEOD-79569 | biostudies-arrayexpress

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