Evidence map›Paper›PMID 38669139›Full record

ArticleSTAR protocols2024

Protocol to process crosslinking and immunoprecipitation data into annotated binding sites.

Shuhao Xu, Grady G Nguyen, Jack T Naritomi, Hema M Kopalle, Brian A Yee, Katherine L Rothamel, Evan A Boyle, Gene W Yeo

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in STAR protocols, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

8 authors.

Shuhao XuDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA.
Grady G NguyenDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA.
Jack T NaritomiDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA.
Hema M KopalleSanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Department of Biological Sciences, University of California, San Diego, La Jolla, CA 92037, USA.
Brian A YeeDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA.
Katherine L RothamelDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Center for RNA Technologies and Therapeutics, UC San Diego, La Jolla, CA 92037, USA.
Evan A BoyleDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
Gene W YeoDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Sanford Stem Cell Institute and Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, UCSD Stem Cell Program, University of California, San Diego, La Jolla, CA 92037, USA; Center for RNA Technologies and Therapeutics, UC San Diego, La Jolla, CA 92037, USA; Sanford Laboratories for Innovative Medicines, La Jolla, CA 92037, USA. Electronic address: geneyeo@ucsd.edu.

Funding

Functional RNA elements in the human genomeR01HG004659 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Kevin Daniel Corbett, Eugene Wei-Ming Yeo · 2008 to 2026
$12.4M
A Comprehensive Functional Map of Human Protein-RNA InteractionsU41HG009889 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R. · 2018 to 2021
$9.4M
Predoctoral and Postdoctoral Training in Cancer Cell BiologyT32CA067754 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI JEAN Y.J. WANG · 1995 to 2026
$6.5M
A comprehensive binding and functional map of human RNA-binding proteinsU24HG009889 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI GRAVELEY, BRENTON R., YEO, EUGENE WEI-MING · 2022 to 2025
$5.5M
Dissecting stress granule dependencies in leukemia stem cellsR01CA273432 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI John T Chang, Eugene Wei-Ming Yeo · 2023 to 2026
$1.8M
NCI NIH HHS R01 CA273432NCI NIH HHS T32 CA067754NHGRI NIH HHS R01 HG004659NHGRI NIH HHS U24 HG009889NHGRI NIH HHS U41 HG009889
6 · The paper itself

Abstract

Here, we present a protocol for using Skipper, a pipeline designed to process crosslinking and immunoprecipitation (CLIP) data into annotated binding sites. We describe steps for partitioning annotated transcript regions and fitting data to a beta-binomial model to call windows of enriched binding. From raw CLIP data, we detail how users can map reproducible RNA-binding sites to call enriched windows and perform downstream analysis. This protocol supports optional customizations for different use cases. For complete details on the use and execution of this protocol, please refer to Boyle et al.

Indexed as

ImmunoprecipitationBinding SitesCross-Linking ReagentsHumansRNASoftwareCross-Linking ReagentsRNABioinformaticsGene ExpressionGenomicsRNA-seqSequence analysis

Identifiers

PMID38669139
PMCPMC11066461

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

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.