Search publications
9 results for “CLIP-seq”
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Identification of RBP binding sites using RNA deaminases.
Methods in enzymology · 2025 · 713: 287-297
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing. Identification of their binding sites has important implications for their physiological and disease-related functions. Crosslinking and immunoprecipitation, followed by sequencing (CLIP-seq) and its derivatives, are the most commonly …
PMID 40250958 DOI ↗
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Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites.
Cell genomics · 2023 · 3(6): 100317
Technology for crosslinking and immunoprecipitation (CLIP) followed by sequencing (CLIP-seq) has identified the transcriptomic targets of hundreds of RNA-binding proteins in cells. To increase the power of existing and future CLIP-seq datasets, we introduce Skipper, an end-to-end workflow that converts …
PMID 37388912 DOI ↗
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Advances and challenges in the detection of transcriptome-wide protein-RNA interactions.
Wiley interdisciplinary reviews. RNA · 2018 · 9(1)
RNA binding proteins (RBPs) play key roles in determining cellular behavior by manipulating the processing of target RNAs. Robust methods are required to detect the numerous binding sites of RBPs across the transcriptome. RNA-immunoprecipitation followed by sequencing (RIP-seq) and crosslinking …
PMID 28853213 DOI ↗
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Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses.
Nature communications · 2016 · 7: 12143
The RNA-binding protein (RBP) TAF15 is implicated in amyotrophic lateral sclerosis (ALS). To compare TAF15 function to that of two ALS-associated RBPs, FUS and TDP-43, we integrate CLIP-seq and RNA Bind-N-Seq technologies, and show that TAF15 binds to ∼4,900 RNAs …
PMID 27378374 DOI ↗
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Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing.
Molecular cell · 2013 · 50(2): 223-35
SR proteins are well-characterized RNA binding proteins that promote exon inclusion by binding to exonic splicing enhancers (ESEs). However, it has been unclear whether regulatory rules deduced on model genes apply generally to activities of SR proteins in the cell. …
PMID 23562324 DOI ↗
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LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
Molecular cell · 2012 · 48(2): 195-206
LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) …
PMID 22959275 DOI ↗
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Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.
Cell reports · 2012 · 1(2): 167-78
Understanding how RNA binding proteins control the splicing code is fundamental to human biology and disease. Here, we present a comprehensive study to elucidate how heterogeneous nuclear ribonucleoparticle (hnRNP) proteins, among the most abundant RNA binding proteins, coordinate to regulate …
PMID 22574288 DOI ↗
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Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans.
Nature structural & molecular biology · 2010 · 17(2): 173-9
MicroRNAs (miRNAs) regulate gene expression by guiding Argonaute proteins to specific target mRNA sequences. Identification of bona fide miRNA target sites in animals is challenging because of uncertainties regarding the base-pairing requirements between miRNA and target as well as the …
PMID 20062054 DOI ↗
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An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells.
Nature structural & molecular biology · 2009 · 16(2): 130-7
The elucidation of a code for regulated splicing has been a long-standing goal in understanding the control of post-transcriptional gene expression events that are crucial for cell survival, differentiation and development. We decoded functional RNA elements in vivo by constructing …
PMID 19136955 DOI ↗
Datasets 25+
The mRNA decay factor CAR-1 regulates axon regeneration via mitochondrial calcium dynamics
6239 · GPL13657
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
Remodeling of oncogenic transcriptomes by small-molecules targeting the RNA-binding protein NONO
Homo sapiens · GPL24676
Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling
Homo sapiens · GPL24676
SerRS mediates translational readthrough of through engagement of the selenocysteine incorporation machinery
Homo sapiens · GPL30173
RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination
Homo sapiens · GPL15520
Enhanced CLIP (eCLIP) identified differential UPF1 binding sites in mouse neural progenitor cells (NPCs) samples
Mus musculus · GPL24247
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ]
Mus musculus · GPL21103
Aging-linked deterioration of RNA metabolism destabilizes the stress response of neurons [eCLIP-seq]
Mus musculus · GPL24676
Mitochondrial double-stranded RNA triggers chronic stress in aged neurons
Homo sapiens · GPL24676, GPL30173
High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection
Homo sapiens · GPL10999
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - 293T cells]
Homo sapiens · GPL16791
Distinct and shared molecular targets and functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [CLIP-Seq]
Mus musculus · GPL13112
Mapping cell structure across scales by fusing protein images and interactions
Homo sapiens · GPL20301
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [CLIP-Seq]
Homo sapiens · GPL20301
RBM17 Mediates Evasion of Pro-Leukemic Factors from Splicing-coupled NMD to Enforce Leukemic Stem Cell Maintenance
Homo sapiens · GPL20301
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_human]
Homo sapiens · GPL11154
Global Identification of the miR-130a targetome in human HSPC Reveals a Novel Role for TBL1XR1 in Hematopoietic Stem Cell Self-Renewal and t(8;21) AML [CUT&RUN]
Homo sapiens · GPL18573
SONAR discovers RNA binding proteins from analysis of large-scale protein-protein interactomes.
Homo sapiens · GPL20301
LARP4 Is an RNA-Binding Protein That Binds Nuclear-Encoded Mitochondrial mRNAs To Promote Mitochondrial Function
Homo sapiens · GPL20301
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - HepG2/K562 cells]
Homo sapiens · GPL16791
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [array]
Homo sapiens · GPL17585
Tissue-selective restriction of RNA editing of CaV1.3 by splicing factor SRSF9
Homo sapiens · GPL18573
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins (CLIP-Seq)
Homo sapiens · GPL9052
Showing first 25 dataset results.
Analyses 25+
GSE276985 · 2 steps · RIP-Seq · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE104949 · 9 steps · CLIP-seq · geo_data_processing
Transcriptome regulation by PARP13 in basal and antiviral states in human cells. (2024)
GSE232597 · 5 steps · RIP-Seq · code_examples
Large-scale evaluation of the ability of RNA-binding proteins to activate exon inclusion. (2024)
GSE240521 · 9 steps · RIP-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE50178 · 6 steps · CLIP-seq · geo_data_processing
ePRINT: exonuclease assisted mapping of protein-RNA interactions. (2024)
GSE180686 · 20 steps · RIP-Seq · code_examples
Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq. (2022)
GSE118347 · 10 steps · CLIP-seq · geo_data_processing
Gain-of-function cardiomyopathic mutations in RBM20 rewire splicing regulation and re-distribute ribonucleoprotein granules within processing bodies. (2021)
GSE107895 · 32 steps · RIP-Seq · code_examples
Widespread RNA editing dysregulation in brains from autistic individuals. (2019)
GSE112782 · 5 steps · RIP-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE125809 · 6 steps · RIP-Seq · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE90650 · 6 steps · CLIP-seq · geo_data_processing
NEAT1 scaffolds RNA-binding proteins and the Microprocessor to globally enhance pri-miRNA processing. (2017)
GSE69583 · 7 steps · CLIP-seq · geo_data_processing
Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells. (2016)
GSE77699 · 2 steps · CLIP-seq · geo_data_processing
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. (2016)
GSE77700 · 3 steps · RIP-Seq · code_examples
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. (2016)
GSE77702 · 5 steps · CLIP-seq · geo_data_processing
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. (2016)
GSE77703 · 5 steps · CLIP-seq · geo_data_processing
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. (2016)
GSE77704 · 5 steps · CLIP-seq · geo_data_processing
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. (2016)
GSE78507 · 33 steps · OTHER · code_examples
Enhanced CLIP Uncovers IMP Protein-RNA Targets in Human Pluripotent Stem Cells Important for Cell Adhesion and Survival. (2016)
GSE86041 · 7 steps · RIP-Seq · code_examples
Protein-RNA Networks Regulated by Normal and ALS-Associated Mutant HNRNPA2B1 in the Nervous System. (2016)
GSE69584 · 8 steps · OTHER · code_examples
Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity. (2015)
GSE69585 · 5 steps · CLIP-seq · geo_data_processing
Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity. (2015)
GSE69586 · 8 steps · CLIP-seq · geo_data_processing
Target Discrimination in Nonsense-Mediated mRNA Decay Requires Upf1 ATPase Activity. (2015)
GSE44591 · 1 step · CLIP-seq · geo_data_processing
Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. (2013)
GSE34993 · 2 steps · RNA-Seq · code_examples
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. (2012)
GSE39872 · 3 steps · CLIP-seq · geo_data_processing
LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance. (2012)
Showing first 25 analysis results.