Abstract:
:High-throughput transcriptional analysis has unveiled a myriad of novel RNAs. However, technical constraints in RNA sequencing library preparation and platform performance hamper the identification of rare transcripts contained within the RNA repertoire. Herein we present targeted-RNA directional sequencing (TARDIS), a hybridization-based method that allows subsets of RNAs contained within the transcriptome to be interrogated independently of transcript length, function, the presence or absence of poly-A tracts, or the mechanism of biogenesis. TARDIS is a modular protocol that is subdivided into four main phases, including the generation of random DNA traps covering the region of interest, purification of input RNA material, DNA trap-based RNA capture, and finally RNA-sequencing library construction. Importantly, coupling RNA capture to strand-specific RNA sequencing enables robust identification and reconstruction of novel transcripts, the definition of sense and antisense RNA pairs and, by the concomitant analysis of long and natural small RNA pools, it allows the user to infer potential precursor-product relations. TARDIS takes ∼10 d to implement.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Portal MM,Pavet V,Erb C,Gronemeyer Hdoi
10.1038/nprot.2015.120subject
Has Abstractpub_date
2015-12-01 00:00:00pages
1915-38issue
12eissn
1754-2189issn
1750-2799pii
nprot.2015.120journal_volume
10pub_type
杂志文章相关文献
Nature Protocols文献大全abstract::The plant cell wall is a chemically complex structure composed mostly of polysaccharides. Detailed analyses of these cell wall polysaccharides are essential for our understanding of plant development and for our use of plant biomass (largely wall material) in the food, agriculture, fabric, timber, biofuel and biocompo...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.081
更新日期:2012-09-01 00:00:00
abstract::The rodent malaria parasite Plasmodium chabaudi chabaudi shares many features with human malaria species, including P. falciparum, and is the in vivo model of choice for many aspects of malaria research in the mammalian host, from sequestration of parasitized erythrocytes, to antigenic variation and host immunity and ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2011.313
更新日期:2011-04-01 00:00:00
abstract::The fabrication of 3D tissues retaining the original functions of tissues/organs in vitro is crucial for optimal tissue engineering and regenerative medicine. The fabrication of 3D tissues also contributes to the establishment of in vitro tissue/organ models for drug screening. Our laboratory has developed a fabricati...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.027
更新日期:2012-04-05 00:00:00
abstract::This transformation procedure generates, with high efficiency (70-90%), hairy roots in cultivars, landraces and accessions of Phaseolus vulgaris (common bean) and other Phaseolus spp. Hairy roots rapidly develop after wounding young plantlets with Agrobacterium rhizogenes, at the cotyledon node, and keeping the plants...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.259
更新日期:2007-01-01 00:00:00
abstract::Detailed biochemical analysis of unmanipulated germinal center (GC) B cells has not been achieved. Previously, we designed and used a simple, economical and new magnetic bead separation scheme for the purification of 'untouched' mature GC and non-GC B cells from the spleens of immunized mice and reported the first bio...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2011.344
更新日期:2011-06-09 00:00:00
abstract::This protocol describes the primary culture of individual chromaffin cells derived by enzymatic digestion from the adrenal medulla of the bovine adrenal gland. Since the late 1970s, such cells have provided a useful model system to study neurotransmitter biosynthesis, storage and release in the catecholaminergic syste...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.136
更新日期:2007-01-01 00:00:00
abstract::Gram-negative and Gram-positive bacteria release a variety of membrane vesicles through different formation routes. Knowledge of the structure, molecular cargo and function of bacterial extracellular vesicles (BEVs) is primarily obtained from bacteria cultured in laboratory conditions. BEVs in human body fluids have b...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-019-0236-5
更新日期:2020-01-01 00:00:00
abstract::N-Succinimidyl 3-(di-tert-butyl[(18)F]fluorosilyl)benzoate ([(18)F]SiFB) is a highly reactive prosthetic group for radiolabeling of proteins for use in positron emission tomography (PET). It is similar to N-succinimidyl-4-[(18)F]fluorobenzoate ([(18)F]SFB), the 'gold-standard' prosthetic group for protein (18)F-labeli...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2012.110
更新日期:2012-11-01 00:00:00
abstract::Hi-C is a powerful method that provides pairwise information on genomic regions in spatial proximity in the nucleus. Hi-C requires millions of cells as input and, as genome organization varies from cell to cell, a limitation of Hi-C is that it only provides a population average of genome conformations. We developed si...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2015.127
更新日期:2015-12-01 00:00:00
abstract::This protocol describes an in vitro approach for measuring the kinetics and affinities of interactions between membrane-anchored proteins. This method is particularly established for dissecting the interaction dynamics of cytokines with their receptor subunits. For this purpose, the receptor subunits are tethered in a...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.270
更新日期:2006-01-01 00:00:00
abstract::With the advent of massively parallel sequencing, considerable work has gone into adapting chromosome conformation capture (3C) techniques to study chromosomal architecture at a genome-wide scale. We recently demonstrated that the inactive murine X chromosome adopts a bipartite structure using a novel 3C protocol, ter...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2016.126
更新日期:2016-11-01 00:00:00
abstract::In this report we describe the development of a standardized three-dimensional (3D) system of the human oral mucosa based on an immortalized human oral keratinocyte cell line (OKF6/TERT-2). The procedure takes approximately 2-3 weeks to complete and includes three main stages: preparation of collagen-embedded fibrobla...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.323
更新日期:2006-01-01 00:00:00
abstract::Laser-mediated gene transfection into mammalian cells has recently emerged as a powerful alternative to more traditional transfection techniques. In particular, the use of a femtosecond-pulsed laser operating in the near-infrared (NIR) region has been proven to provide single-cell selectivity, localized delivery, low ...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.071
更新日期:2013-06-01 00:00:00
abstract::In cell affinity chromatography, type-specific cell separation is based on the interaction between cell-surface receptors and an immobilized ligand on a stationary matrix. This protocol describes the preparation of monolithic polyacrylamide and polydimethylacrylamide cryogel affinity matrices that can be used as a gen...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.135
更新日期:2010-11-01 00:00:00
abstract::The effect of genetic mutation on phenotype is of significant interest in genetics. The type of genetic mutation that causes a single amino acid substitution (AAS) in a protein sequence is called a non-synonymous single nucleotide polymorphism (nsSNP). An nsSNP could potentially affect the function of the protein, sub...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.86
更新日期:2009-01-01 00:00:00
abstract::Apoptosis plays a pivotal role in the regulation of cell turnover, and a defect or an excess of apoptosis has been implicated in several human diseases. Apoptosis is activated from an extracellular death signal, or from an internal pathway starting from the endoplasmatic reticulum or the mitochondria. To investigate t...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.397
更新日期:2007-01-01 00:00:00
abstract::This protocol represents a novel enzyme-luminescence method to detect dopamine sensitively and rapidly with high temporal resolution. In principle, dopamine is first oxidized with tyramine oxidase to produce H(2)O(2), and then the produced H(2)O(2) reacts with luminol to generate chemiluminescence in the presence of h...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.158
更新日期:2008-01-01 00:00:00
abstract::Reversible thiol oxidation of cysteine residues occurs in many intracellular catalytic and signaling processes. Here we describe an optimized protocol, which can be completed in ∼5 d, to unambiguously identify specific cysteine residues that are transiently and reversibly oxidized by comparing two complex biological s...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2014.065
更新日期:2014-05-01 00:00:00
abstract::Mass spectrometry (MS)-based proteomics has become the preferred tool for the analysis of protein phosphorylation. To be successful at such an endeavor, there is a requirement for an efficient enrichment of phosphopeptides. This is necessary because of the substoichiometric nature of phosphorylation at a given site an...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2013.010
更新日期:2013-03-01 00:00:00
abstract::Realizing the potential of human embryonic stem cells (hESCs) in research and commercial applications requires generic protocols for culture, expansion and genetic modification that function between multiple lines. Here we describe a feeder-free hESC culture protocol that was tested in 13 independent hESC lines derive...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2008.140
更新日期:2008-01-01 00:00:00
abstract::Transitivity Clustering is a method for the partitioning of biological data into groups of similar objects, such as genes, for instance. It provides integrated access to various functions addressing each step of a typical cluster analysis. To facilitate this, Transitivity Clustering is accessible online and offers thr...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.197
更新日期:2011-03-01 00:00:00
abstract::This protocol details a method for obtaining a considerable number of human mast cells from peripheral blood cells from normal donors without using stem cell mobilization treatment. By using the magnetic cell sorting system, 10(4)-10(5) cells are retrieved in the CD34+ fraction when 100 ml of blood is drawn from a hea...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2006.344
更新日期:2006-01-01 00:00:00
abstract::We describe the implementation and use of an adaptive imaging framework for optimizing spatial resolution and signal strength in a light-sheet microscope. The framework, termed AutoPilot, comprises hardware and software modules for automatically measuring and compensating for mismatches between light-sheet and detecti...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/s41596-018-0043-4
更新日期:2018-11-01 00:00:00
abstract::A protocol for ester condensation between equimolar amounts of carboxylic acids and alcohols catalyzed by bulky diarylammonium pentafluorobenzenesulfonate is described. We also present procedures for the synthesis of N-(2,6-diisopropylphenyl)-N-mesitylammonium pentafluorobenzenesulfonate. The present ester condensatio...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.254
更新日期:2007-01-01 00:00:00
abstract::The colorimetric bio-barcode assay is a red-to-blue color change-based protein detection method with ultrahigh sensitivity. This assay is based on both the bio-barcode amplification method that allows for detecting miniscule amount of targets with attomolar sensitivity and gold nanoparticle-based colorimetric DNA dete...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.201
更新日期:2007-01-01 00:00:00
abstract::Generation of precisely patterned neural cells from human pluripotent stem cells (hPSCs) is instrumental in developing disease models and stem cell therapies. Here, we provide a detailed 16-d protocol for obtaining high-purity ventral midbrain (VM) dopamine (DA) progenitors for intracerebral transplantation into anima...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2017.078
更新日期:2017-09-01 00:00:00
abstract::Cell-to-cell chemical signaling plays multiple roles in coordinating the activity of the functional elements of an organism, with these elements ranging from a three-neuron reflex circuit to the entire animal. In recent years, single-cell mass spectrometry (MS) has enabled the discovery of cell-to-cell signaling molec...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.277
更新日期:2007-01-01 00:00:00
abstract::Cell proliferation may be measured in vivo by quantifying DNA synthesis with isotopically labeled deoxyribonucleotide precursors. Deuterium-labeled glucose is one such precursor which, because it achieves high levels of enrichment for a short period, is well suited to the study of rapidly dividing cells, in contrast t...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2009.117
更新日期:2009-01-01 00:00:00
abstract::This protocol presents the peptide incorporation of environment-sensitive fluorophores derived from the dimethylaminophthalimide family. The procedure utilizes anhydride precursors of 4-dimethylaminophthalimide (4-DMAP) or 6-dimethylaminonaphthalimide (6-DMN), whose syntheses are described in a related protocol from t...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2007.442
更新日期:2007-01-01 00:00:00
abstract::The Golgi apparatus undergoes extensive disassembly during mitosis and reassembly in post-mitotic daughter cells. This process has been mimicked in vitro by treating Golgi membranes with mitotic and interphase cytosol. To determine the minimal machinery that controls the morphological change, we have developed a defin...
journal_title:Nature protocols
pub_type: 杂志文章
doi:10.1038/nprot.2010.38
更新日期:2010-04-01 00:00:00