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3 results for “CLIP”
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Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data.
Cell genomics · 2024 · 4(7): 100603
The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets …
PMID 38955188 DOI ↗
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Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.
Nature communications · 2024 · 15(1): 875
RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Technologies to discover RNA targets of RBPs such as TRIBE (targets of RNA binding proteins identified by editing) and STAMP (surveying targets by APOBEC1 mediated profiling) utilize …
PMID 38287010 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 ↗
Datasets 24
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
A transcriptome-wide divergence in protein translation scales with LIN28B expression
Mus musculus · GPL20301
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
The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [CLIP-Seq]
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
Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces
Homo sapiens · GPL11154
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (5)
Homo sapiens · GPL15520
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (4)
Homo sapiens · GPL24676
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (1)
Homo sapiens · GPL15520
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (2)
Homo sapiens · GPL24676
Expanded repertoire for RNA-editing-based detection for RNA binding protein interactions (3)
Homo sapiens · GPL24676
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_mouse]
Mus musculus · GPL13112
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]
Homo sapiens · GPL16791
The RNA helicase DDX6 regulation in human skeletal myoblasts [eCLIP-seq]
Homo sapiens · GPL20301
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [array]
Mus musculus · GPL13185
Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_Stability]
Homo sapiens · GPL11154
Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites
Homo sapiens · GPL16791
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]
Homo sapiens · GPL20301
Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP
Homo sapiens · GPL18573
Modulation of the DNA/RNA Binding Protein ARID5A Regulates Microglial Activation and Response [eclip]
Homo sapiens · Illumina
Analyses 12
GSE276985 · 2 steps · GSE · code_examples
Neuronal aging causes mislocalization of splicing proteins and unchecked cellular stress. (2025)
GSE205536 · 13 steps · GSE · code_examples
Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data. (2024)
GSE240521 · 9 steps · GSE · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE77634 · 7 steps · GSE · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE91895 · 1 step · GSE · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
3 steps · eCLIP · kb-test-seed
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE149767 · 14 steps · GSE · code_examples
fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins. (2021)
GSE155728 · 21 steps · GSE · code_examples
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)
GSE166402 · 18 steps · GSE · code_examples
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)
GSE112782 · 5 steps · GSE · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE125809 · 6 steps · GSE · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)
GSE77700 · 3 steps · GSE · code_examples
Distinct and shared functions of ALS-associated proteins TDP-43, FUS and TAF15 revealed by multisystem analyses. (2016)