Keyword Analysis & Research: clip seq


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Keyword CPC PCC Volume Score Length of keyword
clip seq0.2919587788
clip1.1618793974
seq1.650.14137753

Keyword Research: People who searched clip seq also searched

Keyword CPC PCC Volume Score
clip-seq1.910.650474
clip sequence1.130.7191651
clip seq database0.770.8184496
clip seq analysis1.51808370
clip seq protocol0.530.8336683
clip seq kit1.74165892
holmqvist clip seq1.850.8204
rna helicase clip seq0.830.941111
cip sequence rule0.240.4768949
cip sequence count1.431373045
cip sequence0.020.561726
clip sentence0.290.1928435
clip sentence examples0.950.2799371
sequence clip art0.60.2522046
premiere pro sequence timeline clip snap0.040.3642855
clip does not match sequence settings0.080.4679626
video clip to image sequence1.370.9960054
image sequence clip1.910.3363211
premiere pro new sequence from clip shortcut0.990.952963
sequence clip reporter1.430.6919367
insert a clip into a sequence premiere1.370.532215
clip-seq analysis1.10.4658411
clip-seq database0.370.635182
clip-seq protocol1.430.6459951

Search Results related to clip seq on Search Engine

  • Cross-linking immunoprecipitation - Wikipedia

    wikipedia.org

    https://en.wikipedia.org/wiki/Cross-linking_immunoprecipitation

    WEBCross-linking and immunoprecipitation (CLIP, or CLIP-seq) is a method used in molecular biology that combines UV crosslinking with immunoprecipitation in order to identify RNA binding sites of proteins on a transcriptome-wide scale, thereby increasing our understanding of post-transcriptional regulatory networks. CLIP can be used either with …

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  • CLIP and complementary methods | Nature Reviews Methods …

    nature.com

    https://www.nature.com/articles/s43586-021-00018-1

    WEBMar 4, 2021 · Protein-centric methods. All CLIP-based methods for determining the binding landscape of RBPs on a transcriptome-wide scale share the following core workflow (Fig. 1).First, RNAs and interacting ...

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  • Transcriptome-wide identification of RNA-binding protein ... - Nature

    nature.com

    https://www.nature.com/articles/s41596-022-00680-z

    WEBMar 28, 2016 · This pipeline also computes rescue and self-consistency ratios, which are quantitative metrics that can be used to gauge reproducibility in both ChIP-seq and CLIP-seq experiments 29,42.

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  • CLIP-Seq to identify targets and interactions of RNA binding proteins

    nih.gov

    https://pubmed.ncbi.nlm.nih.gov/34517957/

    WEBOne of the essential tools for studying erasers, writers, and readers is cross-linking immunoprecipitation followed by high-throughput sequencing (CLIP-seq). This method can detect the sites on endogenous RNAs bound by RNA-binding proteins or RNA modifying enzymes. Essentially, this strategy allows for snapshots of the epitranscriptome and ...

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  • CLIP protocol | Abcam

    abcam.com

    https://www.abcam.com/protocols/uv-cross-linking-and-immunoprecipitation-clip

    WEBCLIP protocol. Print the full protocol. . 1. UV cross linking of tissue culture cells. 1.1. Remove media and add ice-cold PBS to cells (eg use cells grown in a 10 cm plate for three experiments and add 6 ml PBS). 1.2. Remove lid, place on ice and irradiate once with 150 mJ/cm 2 at 254 nm using a Stratalinker.

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  • Practical considerations on performing and analyzing CLIP-seq

    nih.gov

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6387833/

    WEBFeb 2, 2019 · For CLIP-seq data, the results of functional analysis provide clues to understand post-transcriptional regulation, such as modulating mRNA splicing, translation, and degradation under diverse biological settings. When prior knowledge of the RBP’s function is available, the result of GO term and pathway analyses can be used to verify …

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  • Methods to study RNA–protein interactions | Nature Methods

    nature.com

    https://www.nature.com/articles/s41592-019-0330-1

    WEBFeb 25, 2019 · CLIP-seq methods, however, continue to evolve, and represent an active area of protein-centric method innovation. Table 2 Features of selected CLIP methods. Full size table. CLIP-seq analysis.

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  • Improving CLIP-seq data analysis by incorporating transcript

    nih.gov

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7745353/

    WEBDec 17, 2020 · Background. Over the last decade, CLIP-seq (cross-linking and immunoprecipitation followed by next generation sequencing) [] has become the state-of-the-art procedure to experimentally determine the precise transcriptome-wide binding locations of RNA-binding proteins (RBPs).Many variants have been introduced, out of …

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  • CLIPdb: a CLIP-seq database for protein-RNA interactions - PMC

    nih.gov

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4326514/

    WEBFeb 5, 2015 · CLIP-seq technologies (i.e., HITS-CLIP, PAR-CLIP and iCLIP) have proven their power in deciphering complex codes at the single nucleotide level. Here, we presented a useful resource for the reuse and mining of publicly available CLIP-seq data. To our knowledge, CLIPdb is the most comprehensive database available for use in examining …

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  • CLIP-Seq data analysis from pre-processing to motif detection

    galaxyproject.org

    https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/clipseq/tutorial.html

    WEBAug 17, 2018 · Step 2: Quality Control. As for any NGS data analysis, CLIP-seq data must be quality controlled before being aligned to a reference genome. For more detailed information on NGS quality control, check out the tutorial for NGS. One crucial thing to check for CLIP-Seq data is the sequence duplication levels.

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  • PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

    nih.gov

    https://pubmed.ncbi.nlm.nih.gov/24451213/

    WEBJan 22, 2014 · CLIP-seq is widely used to study genome-wide interactions between RNA-binding proteins and RNAs. However, there are few tools available to analyze CLIP-seq data, thus creating a bottleneck to the implementation of this methodology. Here, we present PIPE-CLIP, a Galaxy framework-based comprehensive o …

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  • easyCLIP analysis of RNA-protein interactions incorporating

    nature.com

    https://www.nature.com/articles/s41467-021-21623-4

    WEBMar 10, 2021 · Library preparation by easyCLIP. To generate a simpler and faster way of producing CLIP-seq datasets, a method was developed using on-bead ligations 17,18,19 of 3′ adapters (termed L3) and 5 ...

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  • HITS-CLIP/CLIP-Seq/PTB-Seq - Illumina

    illumina.com

    https://www.illumina.com/science/sequencing-method-explorer/kits-and-arrays/hits-clip-clip-seq-ptb-seq.html

    WEBHITS-CLIP/CLIP-Seq/PTB-Seq RNA. HITS-CLIP/CLIP-Seq/PTB-Seq. Crosslinking and immunoprecipitation (CLIP), with the use of RNase T1 trimming, was first described by Ule et al. 1 and later applied to high-throughput sequencing to map protein-RNA binding sites in vivo. 2 This approach is similar to RIP-Seq but uses crosslinking to stabilize the ...

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  • CLIP-Seq to identify targets and interactions of RNA binding …

    nih.gov

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9073954/

    WEBFor example, CLIP-seq allows for the isolation of RNAs that are bound to specific proteins. In effect, we are narrowing this snapshot to only look at transcripts involved with our target protein of interest. If interested in proteins involved with RNA modifications, we can take a look at the associated transcripts containing specific chemical ...

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  • Towards in silico CLIP-seq: predicting protein-RNA interaction via

    biomedcentral.com

    https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03015-7

    WEBAug 4, 2023 · We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves high generalization on eCLIP, iCLIP and miCLIP assays, outperforming state-of-the-art classifiers. RBPNet performs bias …

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  • Robust transcriptome-wide discovery of RNA-binding protein ... - Nature

    nature.com

    https://www.nature.com/articles/nmeth.3810

    WEBMar 28, 2016 · The enhanced ligation efficiency allowed the generation of two paired controls that improved specificity to CLIP-seq analysis by removing artifacts, which are often observed in CLIP experiments 14,15.

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  • seCLIP-seq – transcriptome-wide identification of RNA ... - RNA-Seq

    rna-seqblog.com

    https://www.rna-seqblog.com/seclip-seq-transcriptome-wide-identification-of-rna-binding-protein-binding-sites/

    WEBMar 25, 2022 · Cross-linking and immunoprecipitation (CLIP) provides a generalizable, transcriptome-wide method by which RBP/RNA complexes are purified and sequenced to identify sites of intermolecular contact. By simplifying technical challenges in prior CLIP methods and incorporating the generation of and quantitative comparison against size …

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  • CLIPdb: a CLIP-seq database for protein-RNA interactions

    biomedcentral.com

    https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1273-2

    WEBFeb 5, 2015 · Conclusions. CLIPdb is a more complete and better-curated database focused on CLIP-seq data sets than those currently available, providing genome-wide, high-resolution binding sites. Characterizing the post-transcriptional regulatory networks mediated by RNA-binding proteins is a problem of great interest.

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  • RIP-Seq vs. CLIP-Seq: Introduction, Advantages, and Applications

    cd-genomics.com

    https://www.cd-genomics.com/blog/rip-seq-vs-clip-seq-introduction-advantages-and-applications/

    WEBSep 29, 2020 · Compared with CLIP-Seq, RIP-SEQ does not require conducting UV cross-linking, which makes it easy to operate and guarantee repeatable and accurate results. 3. With wide coverage, protein-binding sites can be screened and identified at the genome-wide range. 4. With high resolution and high-throughput sequencing technology, new …

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  • CLIPSeqTools—a novel bioinformatics CLIP-seq analysis suite

    nih.gov

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691824/

    WEBApr 13, 2015 · RESULTS. The output of a CLIP-seq experiment (Fig. 1 A) is typically one or more data files, most often in the FastQ format that contain sequenced reads.CLIPSeqTools is a suite of tools for the analysis of such data sets. The suite has a modular structure and comprises three toolboxes (Fig. 1 B).The first toolbox, clipseqtools-preprocess, is used …

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  • CLIPSeqTools - University of Pennsylvania

    upenn.edu

    http://mourelatos.med.upenn.edu/clipseqtools/

    WEBDescription. CLIPSeqTools is a collection of command line applications used for the analysis of CLIP-Seq datasets. CLIP-Seq stands for UV cross-linking and immunoprecipitation coupled with high-throughput sequencing. CLIPSeqTools has applications for a wide range of analyses that will give an in depth view of the analysed …

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  • nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP

    nih.gov

    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10565428/

    WEBJul 4, 2023 · CLIP-Seq is widely used to capture RNA-binding protein interactions with their target genes. However, the analysis of CLIP-Seq datasets can be challenging especially for non-experts in the field. The development of pipelines, besides facilitating analysis, provide the added benefit of increased reproducibility and correctness.

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