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T-RHEX-RNAseq – a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries from very low numbers of lysed cells

ABSTRACT: T-RHEX-RNAseq – a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries from very low numbers of lysed cells

PROVIDER: PRJEB56375 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10297679_1.fastq.gz	Fastqsanger.gz
	ERR10297679_2.fastq.gz	Fastqsanger.gz
	ERR10297680_1.fastq.gz	Fastqsanger.gz
	ERR10297680_2.fastq.gz	Fastqsanger.gz
	ERR10297681_1.fastq.gz	Fastqsanger.gz

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T-RHEX-RNAseq - a tagmentation-based, rRNA blocked, random hexamer primed RNAseq method for generating stranded RNAseq libraries directly from very low numbers of lysed cells.

Project description:BackgroundRNA sequencing has become the mainstay for studies of gene expression. Still, analysis of rare cells with random hexamer priming - to allow analysis of a broader range of transcripts - remains challenging.ResultsWe here describe a tagmentation-based, rRNA blocked, random hexamer primed RNAseq approach (T-RHEX-RNAseq) for generating stranded RNAseq libraries from very low numbers of FACS sorted cells without RNA purification steps.ConclusionT-RHEX-RNAseq provides an easy-to-use, time efficient and automation compatible method for generating stranded RNAseq libraries from rare cells.

| S-EPMC10111750 | biostudies-literature

Glucagon receptor blocked liver gene signature

Project description:Glucagon receptor blocked liver gene signature

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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.

2014-07-14 | GSE58652 | GEO

TM3'seq: A Tagmentation-Mediated 3' Sequencing Approach for Improving Scalability of RNAseq Experiments.

Project description:RNA-seq has become the standard tool for collecting genome-wide expression data in diverse fields, from quantitative genetics and medical genomics to ecology and developmental biology. However, RNA-seq library preparation is still prohibitive for many laboratories. Recently, the field of single-cell transcriptomics has reduced costs and increased throughput by adopting early barcoding and pooling of individual samples -producing a single final library containing all samples. In contrast, RNA-seq protocols where each sample is processed individually are significantly more expensive and lower throughput than single-cell approaches. Yet, many projects depend on individual library generation to preserve important samples or for follow-up re-sequencing experiments. Improving on currently available RNA-seq methods we have developed TM3'seq, a 3'-enriched library preparation protocol that uses Tn5 transposase and preserves sample identity at each step. TM3'seq is designed for high-throughput processing of individual samples (96 samples in 6h, with only 3h hands-on time) at a fraction of the cost of commercial kits ($1.5 per sample). The protocol was tested in a range of human and Drosophila melanogaster RNA samples, recovering transcriptomes of the same quality and reliability than the commercial NEBNext kit. We expect that the cost- and time-efficient features of TM3'seq make large-scale RNA-seq experiments more permissive for the entire scientific community.

| S-EPMC6945013 | biostudies-literature

Transposase assisted tagmentation of RNA/DNA hybrid duplexes

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

| PRJNA600433 | ENA

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

Project description:To determine the biological function of ATF4 in the modulation of downstream target genes, we performed Tagmentation (CUT&Tag) assay in HCT 116 (Human colorectal cancer) cells

2022-11-29 | GSE218559 | GEO

Quantum generators of random numbers.

Project description:Generation of random numbers is a central problem for many applications in the field of information processing, including, e.g., cryptography, in classical and quantum regime, but also mathematical modeling, Monte Carlo methods, gambling and many others. Both, the quality of the randomness and efficiency of the random numbers generation process are crucial for the most of these applications. Software produced pseudorandom bit sequences, though sufficiently quick, do not fulfill required randomness quality demands. Hence, the physical hardware methods are intensively developed to generate truly random number sequences for information processing and electronic security application. In the present paper we discuss the idea of the quantum random number generators. We also present a variety of tests utilized to assess the quality of randomness of generated bit sequences. In the experimental part we apply such tests to assess and compare two quantum random number generators, PQ4000KSI (of company ComScire US) and JUR01 (constructed in Wroclaw University of Science and Technology upon the project of The National Center for Research and Development) as well as a pseudorandom generator from the Mathematica Wolfram package. Finally, we present our new prototype of fully operative miniaturized quantum random generator JUR02 producing a random bit sequence with velocity of 1 Mb/s, which successfully passed standard tests of randomness quality (like NIST and Dieharder tests). We also shortly discuss our former concept of an entanglement-based quantum random number generator protocol with unconditionally secure public randomness verification.

| S-EPMC8352985 | biostudies-literature

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.

| EGAS00001000528 | EGA

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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