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 single-cell Hi-C to create snapshots of thousands of chromatin interactions that occur simultaneously in a single cell. To adapt Hi-C to single-cell analysis, we modified the protocol to include in-nucleus ligation. This enables the isolation of single nuclei carrying Hi-C-ligated DNA into separate tubes, followed by reversal of cross-links, capture of biotinylated ligation junctions on streptavidin-coated magnetic beads and PCR amplification of single-cell Hi-C libraries. The entire laboratory protocol can be carried out in 1 week, and although we have demonstrated its use in mouse T helper (TH1) cells, it should be applicable to any cell type or species for which standard Hi-C has been successful. We also developed an analysis pipeline to filter noise and assess the quality of data sets in a few hours. Although the interactome maps produced by single-cell Hi-C are sparse, the data provide useful information to understand cellular variability in nuclear genome organization and chromosome structure. Standard wet and dry laboratory skills in molecular biology and computational analysis are required.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Nagano T,Lubling Y,Yaffe E,Wingett SW,Dean W,Tanay A,Fraser Pdoi
10.1038/nprot.2015.127subject
Has Abstractpub_date
2015-12-01 00:00:00pages
1986-2003issue
12eissn
1754-2189issn
1750-2799pii
nprot.2015.127journal_volume
10pub_type
杂志文章相关文献
Nature Protocols文献大全abstract：:We recently invented a method to produce highly potent siRNAs in Escherichia coli, based on the serendipitous discovery that ectopic expression of p19, a plant viral siRNA-binding protein, stabilizes otherwise unstable bacterial siRNAs, which we named pro-siRNAs for prokaryotic siRNAs. We present a detailed protocol d...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.149
更新日期：2013-12-01 00:00:00
abstract：:Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and p...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.036
更新日期：2016-04-01 00:00:00
abstract：:Freestanding plasmonic nanoparticle (NP) superlattice sheets are novel 2D nanomaterials with tailorable properties that enable their use for broad applications in sensing, anticounterfeit measures, ionic gating, nanophotonics and flat lenses. We recently developed a robust, yet general, two-step drying-mediated approa...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-019-0200-4
更新日期：2019-09-01 00:00:00
abstract：:Live-imaging technology has markedly advanced in the field of neural injury and axon degeneration; however, studies are still predominantly performed in in vitro settings such as cultured neuronal cells or in model organisms such as Caenorhabditis elegans in which axons lack glial wrappings. We recently developed a ne...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.042
更新日期：2013-04-01 00:00:00
abstract：:An optimized procedure for the efficient preparation of 2-heptyl-3-hydroxy-4(1H)-quinolone (Pseudomonas quinolone signal or PQS) and a diverse range of structurally related 2-alkyl-4-quinolones with biological activity is presented. The two-step synthesis begins with the formation of α-chloro ketones by the coupling o...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2012.054
更新日期：2012-05-24 00:00:00
abstract：:Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster o...
journal_title：Nature protocols
pub_type： 杂志文章,评审
doi：10.1038/nprot.2016.104
更新日期：2016-09-01 00:00:00
abstract：:The glycocalyx comprises glycosylated proteins and lipids and fcorms the outermost layer of cells. It is involved in fundamental inter- and intracellular processes, including non-self-cell and self-cell recognition, cell signaling, cellular structure maintenance, and immune protection. Characterization of the glycocal...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-020-0350-4
更新日期：2020-08-01 00:00:00
abstract：:We present a protocol for visualizing and quantifying single mRNA molecules in mammalian (mouse and human) tissues. In the approach described here, sets of about 50 short oligonucleotides, each labeled with a single fluorophore, are hybridized to target mRNAs in tissue sections. Each set binds to a single mRNA molecul...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.109
更新日期：2013-09-01 00:00:00
abstract：:The cytokinesis-block micronucleus cytome assay is a comprehensive system for measuring DNA damage, cytostasis and cytotoxicity. DNA damage events are scored specifically in once-divided binucleated (BN) cells and include (a) micronuclei (MNi), a biomarker of chromosome breakage and/or whole chromosome loss, (b) nucle...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.77
更新日期：2007-01-01 00:00:00
abstract：:This protocol describes a method for converting short single-stranded and double-stranded DNA into libraries compatible with high-throughput sequencing using Illumina technology. This method has primarily been developed to improve sequence retrieval from ancient DNA, but it is also applicable to the sequencing of shor...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.038
更新日期：2013-04-01 00:00:00
abstract：:In order to meaningfully analyze common and rare genetic variants, results from genome-wide association studies (GWASs) of multiple cohorts need to be combined in a meta-analysis in order to obtain enough power. This requires all cohorts to have the same single-nucleotide polymorphisms (SNPs) in their GWASs. To this e...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2015.077
更新日期：2015-09-01 00:00:00
abstract：:The Strep-tag II is an eight-residue minimal peptide sequence (Trp-Ser-His-Pro-Gln-Phe-Glu-Lys) that exhibits intrinsic affinity toward streptavidin and can be fused to recombinant proteins in various fashions. We describe a protocol that enables quick and mild purification of corresponding Strep-tag II fusion protein...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.209
更新日期：2007-01-01 00:00:00
abstract：:The synthesis of an azobenzene amino acid (aa) for use as a photo-inducible conformational switch in polypeptides is described. The compound can be easily incorporated into an aa sequence by solid-phase peptide synthesis using standard 9-fluorenylmethoxycarbonyl methods. A reversible conformational change of the pepti...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.488
更新日期：2007-01-01 00:00:00
abstract：:Systematic complex genetic interaction studies have provided insight into high-order functional redundancies and genetic network wiring of the cell. Here, we describe a method for screening and quantifying trigenic interactions from ordered arrays of yeast strains grown on agar plates as individual colonies. The proto...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-020-00456-3
更新日期：2021-01-18 00:00:00
abstract：:The terminal monosaccharide of cell surface glycoconjugates is typically a sialic acid (SA), and aberrant sialylation is involved in several diseases. Several methodological approaches in sample preparation and subsequent analysis using mass spectrometry (MS) have enabled the identification of glycosylation sites and ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2010.167
更新日期：2010-12-01 00:00:00
abstract：:Brachypodium distachyon is emerging as a new model system for bridging research into temperate cereal crops, such as wheat and barley, and for promoting research in novel biomass grasses. Here, we provide an adapter ligation PCR protocol that allows the large-scale characterization of T-DNA insertions into the genome ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2009.32
更新日期：2009-01-01 00:00:00
abstract：:The pig has emerged as an important large animal model in biomedical and pharmaceutical research. We describe a protocol for high-efficiency germline transgenesis and sustained transgene expression in pigs by using the Sleeping Beauty (SB) transposon system. The protocol is based on co-injection of a plasmid encoding ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2014.010
更新日期：2014-04-01 00:00:00
abstract：:This protocol explains how to discover functional signals in genomic sequences by detecting over- or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/). Two typical applications are presented: (i) predicting transcription...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2008.98
更新日期：2008-01-01 00:00:00
abstract：:Telomeres have emerged as crucial cellular elements in aging and various diseases including cancer. To measure the average length of telomere repeats in cells, we describe our protocols that use fluorescent in situ hybridization (FISH) with labeled peptide nucleic acid (PNA) probes specific for telomere repeats in com...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.263
更新日期：2006-01-01 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：:This protocol describes a simple but robust microfluidic assay combining three-dimensional (3D) and two-dimensional (2D) cell culture. The microfluidic platform comprises hydrogel-incorporating chambers between surface-accessible microchannels. By using this platform, well-defined biochemical and biophysical stimuli c...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2012.051
更新日期：2012-06-07 00:00:00
abstract：:An important area of proteomics involves the need for quantification, whether relative or absolute. Many methods now exist for relative quantification, but to support biomarker proteomics and systems biology, absolute quantification rather than relative quantification is required. Absolute quantification usually invol...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.129
更新日期：2006-01-01 00:00:00
abstract：:Accurate analysis of DNA sequence variation in not only humans and animals but also other organisms has played a significant role in expanding our knowledge about genetic variety and diversity in a number of different biological areas. The search for an understanding of the causes of genetic variants and mutations has...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.407
更新日期：2007-01-01 00:00:00
abstract：:This protocol measures externalization of aminophospholipids (APLs) to the outside of the plasma membrane using mass spectrometry (MS). APL externalization occurs in numerous events, and it is relevant for transplant medicine, immunity and cancer. In this protocol, externalized APLs are chemically modified by using a ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.163
更新日期：2014-01-01 00:00:00
abstract：:Although lung transplant is a life-saving therapy for some patients, primary graft dysfunction (PGD) is a leading cause of mortality and morbidity soon after a transplant. Ischemia reperfusion injury is known to be one of the most critical factors in PGD development. PGD is by definition an acute lung injury syndrome ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-018-0019-4
更新日期：2018-08-01 00:00:00
abstract：:Desorption electrospray ionization (DESI) allows the direct analysis of ordinary objects or pre-processed samples under ambient conditions. Among other applications, DESI is used to identify and record spatial distributions of lipids and drug molecules in biological tissue sections. This technique does not require sam...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2008.11
更新日期：2008-01-01 00:00:00
abstract：:New technologies have recently enabled saturation mutagenesis and functional analysis of nearly all possible variants of regulatory elements or proteins of interest in single experiments. Here we discuss the past, present, and future of such multiplexed (functional) assays for variant effects (MAVEs). MAVEs provide de...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.135
更新日期：2016-10-01 00:00:00
abstract：:Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants, animals, marine ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2011.456
更新日期：2012-02-16 00:00:00
abstract：:In situ mRNA hybridization is one of the most powerful techniques for analyzing patterns of gene expression. However, its usefulness is limited in complex plant tissues by the need to fix, embed and section samples before localizing the desired mRNA. Here we present a robust whole-mount in situ hybridization method th...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2014.162
更新日期：2014-10-01 00:00:00
abstract：:The combination of ChIP-seq and transcriptome analysis is a compelling approach to unravel the regulation of gene expression. Several recently published methods combine transcription factor (TF) binding and gene expression for target prediction, but few of them provide an efficient software package for the community. ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.150
更新日期：2013-12-01 00:00:00
