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2 results for “eCLIP”
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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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fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins.
STAR protocols · 2021 · 2(3): 100762
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) structure probing techniques characterize the secondary structure of RNA molecules, which influence their functions and interactions. A variation of SHAPE, footprinting SHAPE (fSHAPE), probes RNA in the presence and absence of protein …
PMID 34485935 DOI ↗
Datasets 11
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
Footprinting SHAPE-eCLIP reveals transcriptome-wide hydrogen bonds at RNA-protein interfaces
Homo sapiens · GPL11154
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
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 10
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)
GSE125809 · 6 steps · GSE · code_examples
The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis. (2019)