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11 results for “Antibody”
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High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues.
Nature communications · 2024 · 15(1): 7067
RNA-binding proteins (RBPs) have pivotal functions in RNA metabolism, but current methods are limited in retrieving RBP-RNA interactions within endogenous biological contexts. Here, we develop INSCRIBE (IN situ Sensitive Capture of RNA-protein Interactions in Biological Environments), circumventing the challenges through …
PMID 39152130 DOI ↗
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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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Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.
Nature methods · 2023 · 20(1): 65-69
Ultraviolet crosslinking and immunoprecipitation (CLIP) methodologies enable the identification of RNA binding sites of RNA-binding proteins (RBPs). Despite improvements in the library preparation of RNA fragments, the enhanced CLIP (eCLIP) protocol requires 4 days of hands-on time and lacks the …
PMID 36550273 DOI ↗
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RBP Image Database: A resource for the systematic characterization of the subcellular distribution properties of human RNA binding proteins.
Nucleic acids research · 2023 · 51(D1): D1549-D1557
RNA binding proteins (RBPs) are central regulators of gene expression implicated in all facets of RNA metabolism. As such, they play key roles in cellular physiology and disease etiology. Since different steps of post-transcriptional gene expression tend to occur in …
PMID 36321651 DOI ↗
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Antibody-Oligonucleotide Conjugation Using a SPAAC Copper-Free Method Compatible with 10× Genomics' Single-Cell RNA-Seq.
Methods in molecular biology (Clifton, N.J.) · 2022 · 2463: 67-80
Recent advances in multimodal approaches toward single-cell analyses present valuable data points that can complement standard flow cytometry data. In particular, the overlay of cell-surface proteome data with gene expression analysis presents a necessary advancement, particularly in the field of …
PMID 35344168 DOI ↗
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Pre-existing adaptive immunity to the RNA-editing enzyme Cas13d in humans.
Nature medicine · 2022 · 28(7): 1372-1376
RNA-guided RNA-targeting nucleases, such as CRISPR-Cas13 proteins, have therapeutic potential for gene editing. Among Cas13d enzymes, Cas13d from the bacteria Ruminococcus flavefaciens (RfxCas13d) is of particular interest owing to its small size and high specificity. However, the existence of pre-existing …
PMID 35668177 DOI ↗
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Zika virus is transmitted in neural progenitor cells via cell-to-cell spread and infection is inhibited by the autophagy inducer trehalose.
Journal of virology · 2021 · 95(5)
Zika virus (ZIKV) is a mosquito-borne human pathogen that causes congenital Zika syndrome and neurological symptoms in some adults. There are currently no approved treatments or vaccines for ZIKV, and exploration of therapies targeting host processes could avoid viral development …
PMID 33328307 DOI ↗
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Active Protein Neddylation or Ubiquitylation Is Dispensable for Stress Granule Dynamics.
Cell reports · 2019 · 27(5): 1356-1363.e3
Stress granule (SG) formation is frequently accompanied by ubiquitin proteasome system (UPS) impairment and ubiquitylated protein accumulation. SGs, ubiquitin, and UPS components co-localize, but the relationship between the ubiquitin pathway and SGs has not been systematically characterized. We utilize pharmacological …
PMID 31042464 DOI ↗
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Th17 Lymphocytes Induce Neuronal Cell Death in a Human iPSC-Based Model of Parkinson's Disease.
Cell stem cell · 2018 · 23(1): 123-131.e6
Parkinson's disease (PD) is a neurodegenerative disorder characterized by the progressive degeneration of midbrain neurons (MBNs). Recent evidence suggests contribution of the adaptive immune system in PD. Here, we show a role for human T lymphocytes as cell death inducers …
PMID 29979986 DOI ↗
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CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins.
Methods (San Diego, Calif.) · 2017 · 118-119: 50-59
Identification of in vivo direct RNA targets for RNA binding proteins (RBPs) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) using antibodies against endogenous …
PMID 28003131 DOI ↗
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Resources for the Comprehensive Discovery of Functional RNA Elements.
Molecular cell · 2016 · 61(6): 903-13
Transcriptome-wide maps of RNA binding protein (RBP)-RNA interactions by immunoprecipitation (IP)-based methods such as RNA IP (RIP) and crosslinking and IP (CLIP) are key starting points for evaluating the molecular roles of the thousands of human RBPs. A significant bottleneck …
PMID 26990993 DOI ↗
Datasets 19
Foxo1 regulates intestinal tissue-resident memory CD8 T cell biology in an anatomic compartment- and context-specific manner
GPL24247
Active ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells
Homo sapiens · GPL16791
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
Homo sapiens · GPL15520
Mutant FUS and ELAVL4 (HuD) aberrant crosstalk in Amyotrophic Lateral Sclerosis
Homo sapiens · GPL20301
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 [in_situ_STAMP]
Mus musculus · GPL24247
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ]
Mus musculus · GPL21103
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isSTAMP]
Mus musculus · GPL30172
Systematic identification of RNA-binding proteins and tethered domains that activate exon splicing inclusion [eCLIP-seq]
Homo sapiens · GPL24676
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isstamp_lr]
Homo sapiens · GPL34382
CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins
Homo sapiens · GPL20301
Biallelic mutations in the 3â exonuclease TOE1 cause Pontocerebellar Hypoplasia Type 7 and result in snRNA processing defects
Homo sapiens · GPL15520
Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP
Homo sapiens · GPL18573
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP - Long-Read]"
Homo sapiens · GPL28352
Musashi-1 is a master regulator of aberrant translation in Group 3 medulloblastoma
Homo sapiens · GPL11154
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II]
Homo sapiens · GPL30173
Analyses 2
GSE122425 · 5 steps · RNA-Seq · code_examples
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)
GSE205536 · 13 steps · OTHER · code_examples
Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP. (2023)