Search publications
8 results for “STAMP”
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Single-cell and isoform-specific translational profiling of the mouse brain.
Nature · 2026
The brain displays the richest repertoire of post-transcriptional mechanisms regulating mRNA translation<sup>1-11</sup>. Among these, alternative splicing has been shown to drive cell-type specificity and, when disrupted, is strongly linked to neurological disorders<sup>12-17</sup>. However, genome-wide measurements of mRNA translation with isoform …
PMID 41708856 DOI ↗
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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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Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.
Genome research · 2024 · 34(11): 2012-2024
Transcription and translation are intertwined processes in which mRNA isoforms are crucial intermediaries. However, methodological limitations in analyzing translation at the mRNA isoform level have left gaps in our understanding of critical biological processes. To address these gaps, we developed …
PMID 38906680 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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FLARE: a fast and flexible workflow for identifying RNA editing foci.
BMC bioinformatics · 2023 · 24(1): 370
Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable …
PMID 37784060 DOI ↗
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Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies.
bioRxiv : the preprint server for biology · 2023
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 37808757 DOI ↗
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Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer.
Molecular cell · 2021 · 81(15): 3048-3064.e9
RNA-binding proteins (RBPs) are critical regulators of post-transcriptional gene expression, and aberrant RBP-RNA interactions can promote cancer progression. Here, we interrogate the function of RBPs in cancer using pooled CRISPR-Cas9 screening and identify 57 RBP candidates with distinct roles in …
PMID 34216543 DOI ↗
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Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes.
Nature methods · 2021 · 18(5): 507-519
RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets …
PMID 33963355 DOI ↗
Datasets 25+
Single-cell and isoform-specific translational profiling of the mouse brain with long-read sequencing [scRNA-Seq, longread]
GPL34585
Single-cell and isoform-specific translational profiling of the mouse brain [scRNA-seq]
GPL34475
Single cell and isoform-specific translational profiling of the mouse brain [ribostamp]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Bulk RNA-seq]
GPL24247
Single cell and isoform-specific translational profiling of the mouse brain [Ribo-STAMP]
GPL24247
Inhibition of YTHDF2 triggers proteotoxic cell death in MYC-driven breast cancer
Homo sapiens · GPL20301
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
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_pacbio]
Homo sapiens · GPL28352
Expanded repertoire of RNA-editing-based detection for RNA binding protein interactions (5)
Homo sapiens · GPL15520
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [NP]
Homo sapiens · GPL24106
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
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [scRNA-seq]
Homo sapiens · GPL24676
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
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [RNA-seq]
Homo sapiens · GPL20301
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [tia1_eclip]
Homo sapiens · GPL16791
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes
Homo sapiens · GPL16791
An in situ method for identification of transcriptome-wide protein-RNA interactions in cells [isstamp_lr]
Homo sapiens · GPL34382
Ribo-STAMP reveals translation status of RNAs bound by PABPN and PABPC
Homo sapiens · GPL24676
Robust single-cell discovery of RNA targets of RNA binding proteins and ribosomes [STAMP_new_eclip]
Homo sapiens · GPL20301
Long-read Ribo-STAMP simultaneously measures transcription and translation at full length isoform resolution
Homo sapiens · GPL28352
Integrated multi-omics analysis of zinc finger proteins uncovers roles in RNA regulation [Ribo-STAMP cell lines]
Homo sapiens · GPL24676
Showing first 25 dataset results.
Analyses 12
GSE275091 · 1 step · RNA-Seq · code_examples
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE276504 · 1 step · geo_data_processing
Single-cell and isoform-specific translational profiling of the mouse brain. (2026)
GSE240014 · 6 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE240325 · 7 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE248461 · 6 steps · RNA-Seq · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE255844 · 5 steps · RNA-Seq · code_examples
Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution. (2024)
GSE263371 · 6 steps · OTHER · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE263870 · 9 steps · OTHER · code_examples
High-sensitivity in situ capture of endogenous RNA-protein interactions in fixed cells and primary tissues. (2024)
GSE277161 · 4 steps · RNA-Seq · code_examples
Integrated multi-omics analysis of zinc-finger proteins uncovers roles in RNA regulation. (2024)
GSE195494 · 5 steps · RIP-Seq · code_examples
Nuclear and cytoplasmic poly(A) binding proteins (PABPs) favor distinct transcripts and isoforms. (2022)
GSE166402 · 18 steps · RIP-Seq · code_examples
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)
GSE166404 · 9 steps · OTHER · code_examples
Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes. (2021)