• mRNA
  • Translation complex profile sequencing (TCP-seq) is a molecular biology method for obtaining snapshots of momentary distribution of protein synthesis complexes along messenger RNA (mRNA) chains. (wikipedia.org)
  • In case of TCP-seq, ribosomes and ribosomal subunits engaged in interaction with mRNA are first fast chemically crosslinked to it with formaldehyde to preserve existing state of interactions ("snapshot" of distribution) and to block any possible non-equilibrium processes. (wikipedia.org)
  • In addition to mRNA transcripts, RNA-Seq can look at different populations of RNA to include total RNA, small RNA, such as miRNA, tRNA, and ribosomal profiling. (wikipedia.org)
  • As a proof of concept, the authors of G&T-seq demonstrated its ability to acquire both the messenger RNA (mRNA) and genomic DNA (gDNA) by using paramagnetic beads with biotinylated oligo-deoxy-Thymine(dT) primer to separate the polyadenylated (Poly-A) RNA from its gDNA prior to amplification and library preparation. (wikipedia.org)
  • ChIP-Seq
  • ChIP-Seq has become a robust, routine and comprehensive technique for investigating and measuring various post-translational histone modifications across the entire genome. (news-medical.net)
  • A common approach in ChIP-Seq analysis is to obtain ChIP-Seq profiles for an experimental sample (disease sample) and a reference sample (healthy sample) and compare them to identify differences in the histone modification patterns. (news-medical.net)
  • TCP-seq thus can be considered more as a functional equivalent of ChIP-seq and similar methods of investigating momentary interactions of DNA that are redesigned to be applicable for translation. (wikipedia.org)
  • ChIP-seq uses immunoprecipitation to isolate specific transcription factors bound to DNA fragments. (wikipedia.org)
  • It is also known as "Input" in the Chip-Seq protocol, since it follows the same steps except it doesn't require immunoprecipitation. (wikipedia.org)
  • When combined with other chromatin analysis techniques such as ChIP-seq, Chem-seq can be utilized to investigate the genome-wide effects of therapeutic modalities and to understand the effects of drugs on nuclear architecture in various biological contexts. (wikipedia.org)
  • In the first two trials, Chem-seq signals occurred at genomic sites occupied by the drugs' corresponding target proteins and were concordant with ChIP-seq results. (wikipedia.org)
  • It can be used in conjunction with ChIP-seq to cross reference the location of certain drugs with DNA binding proteins, like transcription factors, to discover novel interactions and aid in characterizing the molecular mechanisms through which small molecules affect the genome. (wikipedia.org)
  • genome
  • Development of STARR-seq help to identify enhancers in a direct, quantitative and genome-wide manner. (wikipedia.org)
  • An ATAC-seq experiment will typically produce millions of next generation sequencing reads that can be successfully mapped on the reference genome. (wikipedia.org)
  • Regions of the genome where DNA was accessible during the experiment will contain significantly more sequencing reads (since that is where the transposase preferentially acts), and form peaks in the ATAC-seq signal that are detectable with peak calling tools. (wikipedia.org)
  • CAPP-Seq was designed to lower sequencing costs by only targeting specific areas of the genome that are recurrently mutated for a given cancer. (wikipedia.org)
  • DRIP-seq is mainly used for genome-wide mapping of R-loops. (wikipedia.org)
  • DRIP-seq was first used for genome-wide profiling of R-loops in humans, which showed widespread R-loop formation at CpG island promoters. (wikipedia.org)
  • The more recently developed ATAC-seq employs the Tn5 transposase, which inserts specified fragments or transposons into accessible regions of the genome to identify and sequence open chromatin. (wikipedia.org)
  • ChiRP-Seq (Chromatin Isolation by RNA purification) is a high-throughput sequencing method to discover regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest). (wikipedia.org)
  • ChiRP-Seq is one of these new methods which uses the massively parallel sequencing capability of 2nd generation sequencers to catalog the binding sites of these novel RNA molecules on a genome. (wikipedia.org)
  • Sono-Seq (Sonication of Cross-linked Chromatin Sequencing) is a method in molecular biology used for determining the sequences of those DNA regions in the genome near regions of open chromatin of expressed genes. (wikipedia.org)
  • Chem-seq is a technique that is used to map genome-wide interactions between small molecules and their protein targets in the chromatin of eukaryotic cell nuclei. (wikipedia.org)
  • Chem-seq was tested on three classes of drugs using MM1.S multiple myeloma cells to: 1) Investigate the genome-wide binding of the bromodomain inhibitor JQ1 to the BET bromodomain family members BRD2, BRD3 and BRD4 2) Map the genomic binding sites of AT7519, an inhibitor of the cyclin dependent kinase CDK9, and 3) Study how the DNA intercalating agent psoralen interacts with genomic DNA in vivo. (wikipedia.org)
  • Advantages Chem-seq is the first method that provides researchers with a way of determining the location of small molecules throughout the genome. (wikipedia.org)
  • Previously, another similar technique known as chromatin affinity-precipitation (ChAP) assay was used to map the sites of interaction of metabolic compounds in the yeast genome, but Chem-seq is the first method to assess the genome-wide localization of small molecules in mammalian cells. (wikipedia.org)
  • G&T-seq (single cell genome and transcriptome sequencing) is a novel form of single cell sequencing technique allowing one to simultaneously obtain both transcriptomic and genomic data from single cells, allowing for direct comparison of gene expression data to its corresponding genomic data in the same cell. (wikipedia.org)
  • The authors that developed G&T-seq utilized and validated two methods for whole-genome amplification: Multiple displacement amplification and PicoPlex. (wikipedia.org)
  • The authors of the G&T technique found that, though MDA used in G&T-seq yielded genomic coverage of similar breadth as MDA performed in conventional single cell sequencing, the distribution of read coverage was less even across the genome. (wikipedia.org)
  • genomic
  • The key part of the ATAC-seq procedure is the action of the transposase Tn5 on the genomic DNA of the sample. (wikipedia.org)
  • For example, genomic targets of enhancer RNA which act at a distance from their site of synthesis can be easily evaluated by ChiRP-Seq. (wikipedia.org)
  • Genomic regions enriched in the Chem-seq library relative to the control are associated with the small molecule under study. (wikipedia.org)
  • In a third experiment, Chem-seq was efficient in mapping genomic binding sites of the DNA intercalating agent psoralen and showed that bio-psoralen preferentially binds to the transcription start site of active genes. (wikipedia.org)
  • downstream
  • Therefore, a careful and non-redundant design of selector is the vital part in CAPP-Seq and also the size of the selector is related to its downstream costs. (wikipedia.org)
  • facilitates
  • For example, the CRISPR-seq paper demonstrated the feasibility of in vivo studies using this technology, and the CROP-seq protocol facilitates large screens by providing a vector that makes the guide RNA itself readable (rather than relying on expressed barcodes), which allows for single-step guide RNA cloning. (wikipedia.org)
  • Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression over time, or differences in gene expression in different groups or treatments. (wikipedia.org)
  • method
  • In October 2016, the CROP-seq method for single-cell CRISPR screening was presented in a preprint on bioRxiv and later published in the Nature Methods journal. (wikipedia.org)
  • The development of SMiLE-seq technology has provided an attractive alternative method with the potential to facilitate identification and characterization of previously undescribed transcription factor-DNA binding interactions. (wikipedia.org)
  • biases
  • After the first step of variant calling, germline and loss of heterozygosity (LOH) mutations are removed in CAPP-seq to reduce the background biases. (wikipedia.org)
  • vivo
  • In vivo Chem-seq During In vivo Chem-seq, cultured cells in medium are treated simultaneously with either a biotinylated version of the small molecule under study or DMSO (as a control) and 1% formaldehyde for the crosslinking of DNA, proteins and small molecules. (wikipedia.org)
  • isolate
  • Droplet-based microfluidics platforms (or other cell sorting and separating techniques) are used to isolate individual cells, and then scRNA-seq is performed to generate gene expression profiles for each cell. (wikipedia.org)
  • genes
  • The Perturb-seq protocol uses CRISPR technology to inactivate specific genes and DNA barcoding of each guide RNA to allow for all perturbations to be pooled together and later deconvoluted, with assignment of each phenotype to a specific guide RNA. (wikipedia.org)
  • Indirectly, DRIP-seq can be performed on mutant cell lines deficient in genes involved in R-loop resolution. (wikipedia.org)
  • Queensland
  • The SEQ Water Grid is a region-wide, long term, water supply scheme that provides a sustainable water infrastructure network for the South East region of Queensland, Australia. (wikipedia.org)
  • advantages
  • This chapter provides an overview of the development and technical background of transcriptomics and the advantages and limitations of RNA-Seq. (springer.com)
  • The advantages of ATAC-seq include: Low requirements on the amount of the biological sample. (wikipedia.org)
  • sequence
  • On Unix-like computer systems, seq is a utility for generating a sequence of numbers. (wikipedia.org)
  • In its most basic use case, seq N prints out all the integers from 1 to N in sequence. (wikipedia.org)
  • seq was therefore used to generate such a list, as in this example: # Remove file1 through file17: for n in `seq 17` do rm file$n done seq had additional options for controlling the start (not just end) of the numeric sequence, its increment (a floating point number), and the formatting of the number. (wikipedia.org)
  • regions
  • Inside the regions where the ATAC-seq signal is enriched, one can also observe sub-regions with depleted signal. (wikipedia.org)
  • detection
  • A series of steps are involved in analysis of CAPP-Seq data from mutation detection to validation and open source software can do most of the analysis. (wikipedia.org)
  • technology
  • We also review research and potential clinical applications of RNA-Seq technology in inherited, chronic, neoplastic, and infectious diseases. (springer.com)
  • similar
  • A third paper describing a conceptually similar approach (termed CRISP-seq) was also published in the same issue. (wikipedia.org)
  • several
  • While each paper shared the core principles of combining CRISPR mediated perturbation with scRNA-seq, their experimental, technological and analytical approaches differed in several aspects, to explore distinct biological questions, demonstrating the broad utility of this methodology. (wikipedia.org)
  • tool
  • Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. (springer.com)
  • With other alternatives available (e.g., expr), and with more recent shells adding builtin numeric iteration, seq is a rarely used tool today. (wikipedia.org)