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2 results for “Antibody”

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  1. 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 ↗

  2. 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 ↗

Datasets 8

GSE112353 GSE · GEO

Active ribosome profiling with RiboLace and standard ribosome profiling in HEK-293 cells

Homo sapiens · GPL16791

GSE240014 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP]

Mus musculus · GPL24247

GSE240521 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [eCLIP-seq ]

Mus musculus · GPL21103

GSE263371 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isSTAMP]

Mus musculus · GPL30172

GSE263870 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isstamp_lr]

Homo sapiens · GPL34382

GSE205536 GSE · GEO

Multiplexed transcriptome discovery of RNA binding protein binding sites by antibody-barcode eCLIP

Homo sapiens · GPL18573

GSE240325 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP - Long-Read]"

Homo sapiens · GPL28352

GSE248461 GSE · GEO

An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [in_situ_STAMP II]

Homo sapiens · GPL30173

Analyses 1

GSE205536 Processing Pipeline

GSE205536 · 13 steps · GSE · code_examples

Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data. (2024)