Evidence map›Paper›PMID 41455104›Full record

ArticleSTAR protocols2026

Protocol for evaluating RNA-protein associations in mammalian cells with RIP-seq and RIP-qPCR.

Jackson B Trotman, Shuang Li, Quinn E Eberhard, Zhiyue Zhang, J Mauro Calabrese

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Review
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Jackson B TrotmanDepartment of Pharmacology, RNA Discovery Center, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: jbt@unc.edu.
Shuang LiDepartment of Pharmacology, RNA Discovery Center, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Quinn E EberhardDepartment of Pharmacology, RNA Discovery Center, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
Zhiyue ZhangDepartment of Pharmacology, RNA Discovery Center, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
J Mauro CalabreseDepartment of Pharmacology, RNA Discovery Center, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: jmcalabr@med.unc.edu.

Funding

Mechanisms of gene silencing induced by long noncoding RNAsR01GM121806 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI CALABRESE, JOSEPH MAURO · 2017 to 2023
$2.3M
Mechanisms of gene regulation by long noncoding RNAsR35GM153293 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Joseph Mauro Calabrese · 2024 to 2026
$1.9M
Cancer Epigenetics Training GrantT32CA217824 · NCI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI WEISSMAN, BERNARD E. · 2017 to 2021
$1.8M
Cooperative control of Polycomb Repressive Complexes by long noncoding RNAs, CpG island DNA, and RNA-binding proteinsR01GM136819 · NIGMS · UNIV OF NORTH CAROLINA CHAPEL HILL · PI CALABRESE, JOSEPH MAURO · 2020 to 2023
$1.5M
Computational tools to study relationships between sequence, structure, and function in lncRNAsF31HG014413 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI Quinn Elise Eberhard · 2025 to 2026
$82k
NCI NIH HHS T32 CA217824NHGRI NIH HHS F31 HG014413NIGMS NIH HHS R01 GM121806NIGMS NIH HHS R01 GM136819NIGMS NIH HHS R35 GM153293
6 · The paper itself

Abstract

RNA-protein interactions drive gene regulation, subcellular organization, and noncoding RNA function. Here, we present a protocol for measuring RNA-protein associations in formaldehyde-crosslinked mammalian cells using RNA immunoprecipitation followed by sequencing (RIP-seq) and quantitative PCR (RIP-qPCR). We include steps and best practices for qualifying reagents, preparing cells, and processing and analyzing data, including a standardized set of steps to quantify signal over noise. This protocol is broadly applicable for the study of RNA-protein interactions in cells. For complete details on the use and execution of this protocol, please refer to Trotman et al.

Indexed as

ImmunoprecipitationReal-Time Polymerase Chain ReactionRNARNA-Binding ProteinsSequence Analysis, RNAAnimalsHumansRNARNA-Binding ProteinsAntibodyBioinformaticsChIP-seqGene expressionRNA-seqSequence analysisSequencing

Identifiers

PMID41455104
PMCPMC12796723

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.